Transcriptional Regulation for Improved Plant Productivity

ABSTRACT

Methods comprising DNA constructs and polynucleotides of functional transcription factors for improving photosynthetic capacity, biomass and/or grain yield and stress tolerance in various crop and model plants, dicots and monocots with the C 3  or C 4  photosynthetic pathways are described herein.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No. 15/897,958, filed Feb. 15, 2018, which is a continuation of U.S. application Ser. No. 14/653,431, filed Jun. 18, 2015, which is the U.S. National Stage of International Application No. PCT/US2013/076308, filed on Dec. 18, 2013, published in English, which claims the benefit of U.S. Provisional Application No. 61/738,675, filed on Dec. 18, 2012, all of which are hereby incorporated by reference.

GOVERNMENT SUPPORT

This invention was made with government support under Award Number DE-EE0004943 awarded by Department of Energy. The government has certain rights in the invention.

REFERENCE TO A “SEQUENCE LISTING,” A TABLE, OR A COMPUTER PROGRAM LISTING APPENDIX SUBMITTED AS AN ASCII TEXT FILE

The material in the ASCII text file, named “YTEN-60124US3-Sequence-Listing ST25.txt”, created Sep. 9, 2019, file size of 180,224 bytes, is hereby incorporated by reference.

BACKGROUND OF THE INVENTION

The increasing size of the global population, the increasing standard of living in emerging nations such as China and the use of renewable resources such as plants to produce biofuels and bio-based chemicals has placed additional pressure on agriculture. These factors together with the limited availability of additional arable land and water resources means that crop productivity or yield is the key to feeding these demands. Agriculture needs to deliver greater output with reduced inputs. In addition to traditional and marker assisted breeding programs there is an increased need for the identification and application of novel genes which can broadly impact crop yield as well as reduce the impact of environmental stress conditions such as drought, frost, heat and salinity and require fewer chemical inputs such as fertilizer, herbicides, pesticides and fungicides. For example, the 2010 worldwide biofuel production (mainly supplied by bioethanol derived from plant carbohydrate sources, such as starch, sugar from maize, sugarcane and biodiesel from plant oil (from palm and soybean)) reached 28 billion gallons of output providing roughly 2.7% of the world's fuels for road transport. One of the keys to achieving higher yield is to enhance the photosynthetic capacity of plants such that more carbon dioxide is fixed per plant together with up-regulating key metabolic pathways leading to increased levels of storage carbohydrates such as starch and sucrose or lipids such as fatty acids and triglycerides (oils) in plant tissues. In the case of biomass crops used for forage or energy production, increasing the total biomass per plant is also a highly desirable outcome. In many cases efforts to increase storage carbohydrates or oil in plants have been focused on genetic modification using genes encoding individual enzymes in specific metabolic pathways i.e. “single enzyme” or metabolic pathway approaches.

Transcription factors (TFs) are considered potential alternatives to “single enzyme” approaches for the manipulation of plant metabolism (Grotewold, 2008, Curr. Opin. Biotechnol. 19: 138-144). They are critical regulators of differential gene expression during plant growth, development and environmental stress responses. Transcription factors either directly interact with genes involved in key biological processes or interact with the regulation of other TFs that then bind to target genes thus achieving high levels of specificity and control. The resulting outcome is a multilayered regulatory network that affects multiple genes and leads to, for example, fine-tuned changes in the flux of key metabolites through interconnected or competing metabolic pathways (Ambavaram et al., 2011, Plant Physiol. 155: 916-931). There is limited information on transcription factors directly involved in the regulation of photosynthesis-related genes in plants, improvement of photosynthetic parameters has been reported in transgenic crop and model plants overexpressing members of the AP2/EREB, bZIP, NF-X1, NF-Y(HAP), and MYB families of TFs (Saibo et al., 2009, Ann. Bot.-London 103: 609-623). Most of these TFs are stress-induced and confer tolerance to an array of abiotic stress factors, such as drought, salinity, high or low temperatures, and photoinhibition (Hussain et al., 2011, Biotechnology Prog. 27: 297-306, see also WO 2005/112608 A2 and U.S. Pat. No. 6,835,540 B2 to Broun). Only a few TFs, such as Dofl and MNF from maize are associated with expression of genes involved in C₄ photosynthesis (Weissmann & Brutnell, 2012, Curr. Opin. Biotechnol. 23: 298-304; Yanagisawa, 2000, Plant J. 21: 281-288). Increased growth of different vegetative and/or floral organs resulting in improved biomass production have been reported in plants overexpressing TFs, such as ARGOS, AINTEGUMENTA, NAC1, ATAF2, MEGAINTEGUMENTA, and ANGUSTIFOLIA (Rojas et al., 2010, GM Crops 1: 137-142 and references therein; see also WO 2011/109661 A1, WO 2010/129501, WO 2009/040665 A2, WO 02/079403 A2 and U.S. Pat. Nos. 7,598,429 B2 to Heard et al. and 7,592,507 B2 to Beekman et al.). Modifications of plant metabolic pathways by altering the expression of transcription factors regulating genes in the biosynthesis of lignin (US 2012/0117691 A1 to Wang et al.) and secondary metabolites (U.S. Pat. No. 6,835,540 B2 to Broun) have also been reported.

Thus, a need exists for identification of transcription factors whose increased or modified expression not only results in increased levels of the light harvesting pigments used in photosynthesis and improved photosynthetic capacity of the plants but which also up-regulate key metabolic pathways resulting in one or more additional desirable effects selected from the group comprising: increased levels of starch, glucose or sucrose (non-structural carbohydrates) in plant tissues; increased levels of fatty acids; increased production of biomass and/or grain yield; and enhanced stress tolerance. It is also desirable to be able to identify suitable variants of such transcription factors in a wide range of crop species and to be able to engineer these genes in a wide range of crops including dicots and monocots with C₃ or C₄ photosynthetic pathways.

Specific crops of interest for practicing this invention include: switchgrass, Miscathus, Medicago, sweet sorghum, grain sorghum, sugarcane, energy cane, elephant grass, maize, wheat, barley, oats, rice, soybean, oil palm, safflower, sesame, flax, cotton, sunflower, Camelina, Brassica napus, Brassica carinata, Brassica juncea, pearl millet, foxtail millet, other grain, oilseed, vegetable, forage, woody and biomass crops.

SUMMARY OF THE INVENTION

This invention is generally in the area of novel genes and methods for increasing plant crop yield using those novel genes. Described herein is the use of novel transcription factors that when overexpressed in a plants of interest affect the regulation of multiple biological pathways in the crop resulting in, for example, higher levels of photosynthetic pigments in green tissue, increased photosynthetic efficiency, increased content of non-structural carbohydrates (starch, sucrose, glucose) and fatty acids in leaf tissues, increased biomass yield and improved stress tolerance.

Screening of a number of transcription factor candidates has resulted in the identification of novel transcription factors that when expressed from a heterologous promoter in transgenic plants results in plants having increased expression of these transcription factors. The increased expression levels can be up to 1.2 fold 1.3 fold, 1.5 fold, 2 fold, 3 fold, 4 fold, 5 fold, 6 fold, 7 fold, 8 fold, a 9 fold or greater than 10 fold the level of background expression found in a wild-type plant (e.g., non-transgenic plant, test plant or control plant). As a result of the increased expression of these transcription factors a number of beneficial traits are achieved including but not limited to: increased levels of photosynthetic pigments; increased photosynthetic capacity; increased levels of non-structural carbohydrates, including starch, sucrose and glucose in plant tissues; increased levels of fatty acids in plant tissues; increased biomass growth rate and yield; and improved stress tolerance in comparison to wild-type plants. Methods for identifying transcription factors and producing the transgenic plants are also described herein. The transcription factor genes, their homologs and/or orthologs and the methods described herein for increasing their expression or for expressing them in heterologous hosts can achieve yield improvements in a wide range of crop plants.

A higher photosynthesis rate in plants transformed with the transcription factors of the invention and their homologs and/or orthologs combined with elevated levels of photosynthetic pigments achieved by the methods described lead to increased accumulation of products of the central carbon metabolism, such as starch, soluble sugars and fatty acids as well as improved biomass and grain production. It is also likely that plants with elevated levels of expression of these transcription factors will also be useful for increasing the production of other products produced in plants by genetic engineering including for example, storage starches. The overall potential impact of increasing the expression of these transcription factors in plants is illustrated in FIG. 1. Improved stress tolerance mediated by the transcription factors of the invention, produce transgenic plants with better agronomic performance under abiotic and biotic stress conditions than non-transformed controls or test plants (also referred to as wild type). In another related aspect, a quick and reliable method for testing the stress response of large populations of transgenic and wild type plants (e.g., crops) is also described. Also described herein are novel gene sequences, polypeptides encoded by them, gene constructs and methods for their use to produce transgenic plants, plant products, crops and seeds.

These transgenic plants, portions of transgenic plants, transgenic crops and transgenic seeds generated by the introduction of or increased expression of the functional transcription factors and their homologs, orthologs and function fragments identified herein have improved photosynthetic capacity, improved biomass production, and/or improved grain yield and stress tolerances compared to wild-type plants.

This invention relates to the identification of transcription factor genes which when expressed to higher levels than is found in wild type plants or expressed in heterologous plants results in one or more desirable traits selected from: higher levels of photosynthetic pigments; higher photosynthetic activity; higher levels of starch and/or sucrose and/or glucose; higher yield of biomass; and improved stress tolerances.

In one aspect of the invention, genes encoding transcription factors belonging to the APETALA2 (AP2)/ETHYLENE RESPONSE FACTOR (ERF) family (e.g., SEQ ID NOs: 1 and 2) and transcription factors from the Nuclear-Factor Y (NF-YB) family (e.g., SEQ ID NO: 3) and their homologues and orthologs from other plant species are described as well as methods of producing transgenic plants overexpressing these transcription factors genes in a wide range of plants to achieve one or more traits selected from: higher levels of photosynthetic pigments; higher photosynthetic activity; higher levels of starch and/or sucrose and/or glucose; higher yield, and improved stress tolerance.

Host plants include but are not limited to food crops, forage crops, bioenergy and biomass crops, perennial and annual plant species. Examples of specific crops of interest for practicing this invention include: switchgrass, Miscathus, Medicago, sweet sorghum, grain sorghum, sugarcane, energy cane, elephant grass, maize, wheat, barley, oats, rice, soybean, oil palm, safflower, sesame, flax, cotton, sunflower, Camelina, Brassica napus, Brassica carinata, Brassica juncea, pearl millet, foxtail millet, other grain, oilseed, vegetable, forage, woody and biomass crops.

In a first aspect, a transgenic plant, or a portion of a plant, or a plant material, or a plant seed, or a plant cell comprising one or more nucleotide sequences encoding one or more AP2/ERF and/or NF-YB transcription factors, wherein the AP2/ERF transcription factor is encoded by the nucleotide sequence of SEQ ID NOs: 1 or 2 and the NF-YB transcription factor is encoded by the nucleotide sequence of SEQ ID NO: 3 and the increased expression of one or more transcription factors is increased resulting in one or more traits selected from: higher levels of photosynthetic pigments; higher photosynthetic activity; higher levels of starch and/or sucrose and/or glucose; higher yield; and improved stress tolerance in the transgenic plant, portion of a plant, plant material, plant seed, or plant cell is described. The increased expression of the transcription factors can be measured in a number of ways including a fold increase over the wild type plant such as 1.5 fold, 2 fold, 3 fold, 4 fold, 5 fold 6 fold 7 fold 8 fold greater than 9 fold higher than the expression of the same gene in a wild type plant. In some cases the increased expression results from the expression of the transcription factor gene through genetic manipulation to express the transcription factor in a heterologous plant host. An example of this particular embodiment would be expressing one of the genes, including homolog or orthologs, isolated from switchgrass in a plant selected from Miscathus, Medicago, sweet sorghum, grain sorghum, sugarcane, energy cane, elephant grass, maize, wheat, barley, oats, rice, soybean, oil palm, safflower, sesame, flax, cotton, sunflower, Camelina, Brassica napus, Brassica carinata, Brassica juncea, pearl millet, foxtail millet, other grain, oilseed, vegetable, forage, woody and biomass crops.

In a first embodiment of the first aspect, the expression of the one or more transcription factors increases the level of photosynthetic pigments including chlorophyll and/or carotenoids. The improvement is compared to a non-transgenic plant and such improvement can be measured in a variety of ways, including a fold increase or percent increase, such as 10%, 20%, 50% or 75%.

In a second embodiment of the first aspect, as compared to the wild type plant, the increased expression of the one or more transcription factors improves the rate of photosynthesis in the plant. The improvement is compared to a non-transgenic plant and such improvement can be measured in a variety of ways, including a fold increase or percent increase, such as 10%, 20%, 30%, 40%, 50% or higher.

In a third embodiment of the first aspect, as compared to the wild type plant, the increased expression of one or more transcription results in increased levels of starch and/or sucrose and/or glucose in the plant tissue. The increase in levels of starch and/or sucrose and/or glucose in the plant tissue alone or in combination can be measured as a % of dry weight of the plant tissue analyzed for example 2%, 3%, 4%, 5%, 10%, 15%, 20% of the dry weight of the plant tissue.

In a fourth embodiment as compared to the wild type plant, the expression of the one or more transcription factors results in plants with higher biomass yields. The improvement is compared to a non-transgenic plant and such improvement can be measured in a variety of ways, percent increase such as 10%, 20%, 50% or greater than 50% increase in the dry weight of the plant as compared to a wild type plant.

In a fifth embodiment as compared to the wild type plant, the expression of one or more transcription factors improves tolerance to one or more abiotic stress factors selected from excess or deficiency of water and/or light, high or low temperature, and high salinity. The improvement is compared to a non-transgenic plant and such improvement can be measured in a variety of ways, including a fold increase or percent increase, such as 10%, 20%, 50% or 75%.

In a second embodiment of the first aspect or of the first embodiment, the transcription factor is encoded by an ortholog, homolog, or functional fragment of SEQ ID NOs: 1, 2, or 3. In a third embodiment of the first aspect or other embodiment, a promoter is operably linked to one or more nucleotide sequence of SEQ ID NOs: 1, 2, or 3 in a plant transformation vector.

In a third embodiment of the first aspect or other embodiment, the plant has increased starch content, soluble sugar content, grain yield, plant size, organ size, leaf size, and/or stem size when compared to a non-transgenic plant.

In a fourth embodiment of the first aspect or other embodiment, the expression of one or more transcription factors increases the production of food crops, feed crops, or crops used in the production of fuels or industrial products, when compared to a non-transgenic plant.

In a second aspect, an isolated nucleotide sequence comprising a nucleic acid sequence encoding an AP2/ERF or an NF-YB transcription factor; wherein the transcription factor is functional in a plant, selected from the group consisting of SEQ ID NOs: 1, 2, and 3; and expression of the transcription factor result in higher levels of starch and/or sucrose and/or glucose in the plant.

In a first embodiment of the second aspect, the expression resulting in higher levels of one or more of starch, sucrose and glucose and higher biomass, or higher levels of one or more of starch, sucrose and glucose with no significant increase in biomass.

In a second embodiment of the second aspect or of the first embodiment of the second aspect, the nucleic acid sequence further comprises at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NOs: 1, 2, or 3.

In a third embodiment of the second aspect or the embodiments, the plant further comprises a temporal promoter for expression of all transcription factors such that the gene is overexpressed one the plant is fully grown and the accumulation of storage materials in the seed is initiated. Methods of screening for plants with this outcome are also contemplated. Alternatively, other select promoters for desirable expression of the transcription factors are contemplated.

In a fourth embodiment of the second aspect or of the embodiments, the expression of the transcription factor increases photosynthetic activity, carbon flow and/or total content of photosynthetic pigments when compared to a non-transgenic plant.

In a fifth embodiment of the second aspect or of any of the other embodiments, the nucleic acid sequence encoding a polypeptide of SEQ ID NOs: 4, 5, or 6.

In a third aspect, a transcription factor, comprising an AP2/ERF or a NF-YB transcription factor polypeptide selected from SEQ ID NOs: 4, 5, and 6; wherein the transcription factor is functional in a plant and the expression of the transcription factor increases a carbon flow in the transgenic plant is described.

In a first embodiment of the third aspect, the transcriptional factor is functional in a C₃ or C₄ dicotyledonous plant, a C₃ or C₄ monocotyledonous plant, In a second embodiment of the third aspect or of any of the other embodiments, the polypeptide sequence further comprises at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NOs: 4, 5, or 6.

In a third embodiment of the third aspect or of any of the other embodiments, the increased carbon flow is due to increased biomass yield, or increased starch, glucose or sucrose in plant tissues when compared to a non-transgenic plant.

In a fourth embodiment of the third aspect or of any of the other embodiments, expression the transcription factor increases photosynthetic activity, carbon flow and/or total content of photosynthetic pigments when compared to a non-transgenic plant.

In a fourth aspect, a biobased transgenic plant product obtained from the transgenic plant of the first aspect and any of the embodiment described having a 100% biobased carbon flow is described. In certain embodiments of this fourth aspect, the product is an article having a biobased content of at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, 90% or 95%.

In a fifth aspect, a method of producing a transgenic plant, comprising coexpressing one or more AP2/ERF and a NF-YB transcription factor, wherein the AP2/ERF transcription factor is encoded by the nucleotide sequence of SEQ ID NOs: 1 or 2 and the NF-YB transcription factor is encoded by the nucleotide sequence of SEQ ID NO: 3 is described.

In a sixth aspect, a method for testing the response of plants to different abiotic stress factors in tissue culture for identification of plants with increased tolerance to the stress factors, comprising comparing a test plant with the transgenic plant of claim 1 under one or more conditions that cause stress including adverse changes in water, light, temperature, and salinity is described.

In a seventh aspect methods for transformation comprising incorporating into the genome of a plant with one or more vectors comprising the nucleotide sequences described herein are described.

In an eighth aspect or of any of the embodiments of the first aspect, the transgenic plant of the first aspect has an increased photochemical quantum yield than the yield of a non-transgenic plant.

In a ninth aspect or of any of the embodiments of the first aspect, the transgenic plant of the first aspect has a starch content (e.g., yield) increased by at least 2 fold greater than the corresponding starch content of a non-transgenic plant.

In a tenth aspect or of any of the embodiments of the first aspect, the transgenic plant of the first aspect has a starch content of at least 2 fold greater to about 4.3 greater than the content of a non-transgenic plant.

In an eleventh aspect or of any of the embodiments of the first aspect, the transgenic plant of the first aspect has a chlorophyll content that is greater than the content of a non-transgenic plant or has a chlorophyll content that is at least 1.1 greater to about 2.5-fold greater than the content of a non-transgenic plant.

In a twelfth aspect or of any of the embodiments of the first aspect, the transgenic plant of the first aspect has a sucrose content that is higher than the content of a non-transgenic plant or a sucrose content that is at least two fold greater to about 4.3 fold greater than the content of a non-transgenic plant.

In a thirteenth aspect or of any of the embodiments of the first aspect, the transgenic plant of the first aspect has an electron transport rate above the rate of a non-transgenic plant.

In a further embodiment of any of the aspects, the plant is selected from switchgrass, Miscathus, Medicago, sweet sorghum, grain sorghum, sugarcane, energy cane, elephant grass, maize, wheat, barley, oats, rice, soybean, oil palm, safflower, sesame, flax, cotton, sunflower, Camelina, Brassica napus, Brassica carinata, Brassica juncea, pearl millet, foxtail millet, other grain, oilseed, vegetable, forage, industrial, woody and biomass crops.

In a further embodiment, transgenic plants of the previous embodiments can be screened to identify plants where the overall biomass yield is similar to the wild type plant but the levels of one or more traits selected from: increased concentration of photosynthetic pigments; increased photosynthesis efficiency; increased levels of starch and/or sucrose and/or glucose; increased levels of fatty acids and increased stress tolerance higher than the levels in the wild-type plants. For example a transgenic plant with a biomass yield similar to a wild type plant but with a cumulative level of starch plus glucose plus sucrose 1.5 fold, 2 fold, 5 fold, 10 fold or more higher can be identified.

In a further embodiment, a screening method for identifying specific genes or combinations of genes which can be used to achieve some of the individual trait improvements is described herein.

In certain embodiments, methods related to upregulation of the central carbon metabolism by PvSTR1, PvSTIF1 and PvBMY1 leading to increased photosynthetic pigments and activity and elevated levels of starch, soluble sugars and fatty acids as well as improved stress tolerance and productivity of plants and plant products are described. These methods include the incorporation of one or more of the transcription factors described by SEQ ID NOs: 1, 2 and 3 and homologs, orthologs and functional fragments thereof. For example, the transgenic plant can comprise SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3, or a homolog, ortholog or functional fragment thereof or any combination of two or more of SEQ ID NO: 1, SEQ ID NO: 2 and SEQ ID NO: 3, including their homologs, orthologs or functional fragments thereof (e.g., SEQ ID NO: 1 and SEQ ID NO: 2; SEQ ID NO: 1 and SEQ ID NO: 3; homolog of SEQ ID NO: 1 and SEQ ID NO: 2; homolog of SEQ ID NO: 1 and a homolog of SEQ ID NO: 2; etc.).

In a fourteenth aspect of the invention, a transgenic plant, or a portion of a plant, or a plant material, or a plant seed, or a plant cell comprising one or more nucleotide sequences encoding a family of AP2/ERF or NF-YB transcription factor, wherein the AP2/ERF transcription factor is encoded by the nucleotide sequence of SEQ ID NOs: 1 or 2 and the NF-YB transcription factor is encoded by the nucleotide sequence of SEQ ID NO: 3; wherein the expression of the one or more transcription factors increases carbon flow in the transgenic plant, portion of a plant, plant material, plant seed, or plant cell is described. In a first embodiment of the fourteenth aspect, the expression of the one or more transcription factors improves tolerance to one or more abiotic stress factors selected from excess or deficiency of water and/or light, from high or low temperature, and high salinity. In a second embodiment of the fourteenth aspect or of the first embodiment of the aspect, the transcription factor is encoded by an ortholog, homolog, or functional fragment encoded by SEQ ID NOs: 1, 2, or 3. In a third embodiment of the fourteenth aspect or of any of the embodiments of the aspect, the transgenic plant, portion of a plant or plant material, plant seed or plant cell, further comprises a vector containing a promoter operably linked to one or more nucleotide sequence of SEQ ID NOs: 1, 2, or 3. In a fourth embodiment of the fourteenth aspect or of any of the embodiments of the aspect the plant is selected from a crop plant, a model plant, a monocotyledonous plant, a dicotyledonous plant, a plant with C3 photosynthesis, a plant with C4 photosynthesis, an annual plant, a perennial plant, a switchgrass plant, a maize plant, or a sugarcane plant. In a fifth embodiment of the fourteenth aspect or of any of the embodiments of the aspect the annual or perennial plant is a bioenergy or biomass plant. In a sixth embodiment of the fourteenth aspect or of any of the embodiments of the aspect expression of one or more transcription factors increases photosynthetic activity, carbon flow and/or total content of photosynthetic pigments. In a seventh embodiment of the fourteenth aspect or of any of the embodiments of the aspect the increased carbon flow results in increased biomass yield when compared to a non-transgenic plant. In an eighth embodiment of the fourteenth aspect or of any of the embodiments of the aspect, wherein the plant has an increase of one or more of the following: starch content, soluble sugars content, grain yield, plant size, organ size, leaf size, and/or stem size when compared to a non-transgenic plant. In a ninth embodiment of the fourteenth aspect or of any of the embodiments of the aspect the expression of one or more transcription factors leads to increases in the production of food crops, feed crops, or crops for the production of fuels or industrial products, when compared to a non-transgenic plant.

In a fifteenth aspect of the invention, an isolated nucleotide sequence comprising a nucleic acid sequence encoding an AP2/ERF or an NF-YB transcription factor; wherein the transcription factor selected from the group consisting of SEQ ID NOs: 1, 2, and 3 is functional in a plant; and expression of the transcription factor increases carbon flow in the transgenic plant is described. In a first embodiment of the fifteenth aspect, the plant is selected from the group consisting of a C3 or C4 dicotyledonous plant, a C3 or C4 monocotyledonous plant, grass, a switchgrass plant, a maize plant, or a sugarcane plant. In a second embodiment of the fifteenth aspect or of any of the embodiments of the aspect, the nucleic acid sequence further comprises at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NOs: 1, 2, or 3. In a third embodiment of the fifteenth aspect or of any of the embodiments of the aspect, the increased biomass yield is due to increased carbon flow when compared to a non-transgenic plant. In a fourth embodiment of the fifteenth aspect or of any of the embodiments of the aspect, expression of the transcription factor increases photosynthetic activity, carbon flow and/or total content of photosynthetic pigments when compared to a non-transgenic plant. In a fifth embodiment of the fifteenth aspect or of any of the embodiments of the aspect, the nucleic acid sequence encodes a polypeptide of SEQ ID NOs: 4, 5, or 6. In a sixth embodiment of the fifteenth aspect or of any of the embodiments of the aspect, the increased carbon flow increases the starch, sucrose and glucose levels in a transgenic plant without the same corresponding increase in biomass yield.

In a sixteenth aspect, a transcription factor, comprising an AP2/ERF or a NF-YB transcription factor polypeptide selected from SEQ ID NOs: 4, 5, and 6; wherein the transcription factor is functional in a plant and the expression of the transcription factor increases a carbon flow in the transgenic plant is described. In a first embodiment of the sixteenth aspect, the plant is selected from the group consisting of a C3 or C4 dicotyledonous plant, a C3 or C4 monocotyledonous plant, grass, or a switchgrass plant, a maize plant, or a sugarcane plant. In a second embodiment of the sixteenth aspect or of the first embodiment of the aspect, the polypeptide sequence further comprises at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NOs: 4, 5, or 6. In a third embodiment of the sixteenth aspect or of the first or second embodiment of the aspect, the increased biomass yield is due to increased carbon flow when compared to a non-transgenic plant. In a fourth embodiment of the sixteenth aspect or of the first, second or third embodiment of the aspect, expression of the transcription factor increases photosynthetic activity, carbon flow and/or total content of photosynthetic pigments when compared to a non-transgenic plant.

In a seventeenth aspect, a method for manufacturing a transgenic seed for producing a crop of transgenic plants with an enhanced trait resulting from the expression of one or more transcription factors or homologs, orthologs or functional fragments thereof, encoded by the nucleotide sequence of SEQ ID NOs: 1, 2 or 3, comprising: a) screening a population of plants transformed with transcription factor(s) for the enhanced trait; b) selecting from the population one or more plants that exhibit the trait; and c) collecting seed from the selected plant is described. In a first embodiment of the seventeenth aspect, the seed is maize seed or sorghum seed and the enhanced trait is seed carbon content.

In an eighteen aspect, a method of producing a transgenic plant, comprising coexpressing one or more AP2/ERF and NF-YB transcription factors in a plant, wherein the AP2/ERF transcription factor is encoded by the nucleotide sequence of SEQ ID NOs: 1 or 2 and the NF-YB transcription factor is encoded by the nucleotide sequence of SEQ ID NO: 3 is described.

In a nineteenth aspect, a method for testing the response of a plant to different stress factors in tissue culture for identification of plants with increased tolerance to the stress factors, comprising comparing a test plant with the transgenic plant of the fourteen aspect under one or more conditions that cause stress including changes in water, light, temperature, and salinity is described. In an embodiment of the seventeenth, eighteen or nineteen aspect, further comprising introducing into a plant one or more vectors comprising the nucleotide sequences of the invention.

In any of the aspects or embodiments described above, the photochemical quantum yield of the plant is at least 2-fold greater than the yield of a corresponding non-transgenic plant. In any of the aspects or embodiments described above, the plant has a starch yield increased by at least 2-fold the content of a corresponding non-transgenic plant. In any of the aspects or embodiments described above, the plant has a starch yield increased by at least 2-fold to about a 4.5-fold content of a corresponding non-transgenic plant. In any of the aspects or embodiments described above, the plant has a chlorophyll content that is 1.5 times greater than the content of a corresponding non-transgenic plant. In any of the aspects or embodiments described above, the plant has a chlorophyll content that is at least 1.5 fold greater to about 2.5 fold greater than the content of a corresponding non-transgenic plant. In any of the aspects or embodiments described above, the plant has a sucrose content that is at least 1.5 fold greater than the content of a corresponding non-transgenic plant. In any of the aspects or embodiments described above, the plant has a sucrose content that is at least two fold greater to about 4.3 fold greater than the content of a corresponding non-transgenic plant. In any of the aspects or embodiments described above, the plant has a plant grown rate increased by at least 10% above the rate of a corresponding non-transgenic plant. In any of the aspects or embodiments described above, the plant is switchgrass, maize, or sugar cane.

In a twentieth aspect, a method for enhancing a trait in a transgenic plant relative to a control non-transgenic plant, comprising: (a) increasing expression of at least one nucleic acid sequence encoding a transcription factor from AP2/ERF and NF-YB families, selected from the nucleic acid sequence of SEQ ID NO: 1, SEQ ID NO: 2, and SEQ ID NO: 3, or an ortholog, homolog or functional fragment thereof; and (b) selecting for a transgenic plant having an enhanced trait relative to a control plant is described. In a first embodiment of the twentieth aspect, the trait is selected from one or more of the following: carbon flow, primary metabolites, tolerance to one or more abiotic stress factors, and one or more photosynthetic pigments.

In a twenty-first aspect, a transgenic plant having a trait modification relative to a corresponding non-transgenic plant, comprising one or more nucleotide sequences encoding a AP2/ERF or NF-YB transcription factors, wherein the AP2/ERF transcription factor is encoded by the nucleotide sequence of SEQ ID NOs: 1 or 2 and the NF-YB transcription factor is encoded by the nucleotide sequence of SEQ ID NO: 3 or a ortholog, homolog, or functional fragment thereof, wherein the trait modification is selected from one or more of the following: carbon flow, levels of photosynthetic pigments; photosynthetic capacity; levels of starch, sucrose and glucose in plant tissues, levels of fatty acids in plant tissues; biomass growth rate and yield; and stress tolerance is described. In a first embodiment of the twenty-first aspect, the trait modification is a greater than 3 fold yield of starch or soluble sugars and the increase in biomass production is less than 1.5 fold.

In a twenty-second aspect, a transgenic maize plant having an increased non-structural carbohydrate content comprising, a) introducing into a plant cell one or more nucleotides encoding AP2/ERF and/or NF-YB transcription factor, wherein the AP2/ERF transcription factor is encoded by the nucleotide sequence of SEQ ID NOs: 1 or 2 and the NF-YB transcription factor is encoded by the nucleotide sequence of SEQ ID NO: 3 or a ortholog, homolog, or functional fragment thereof, and b) producing a transgenic plant from the plant cell having an increased non-structural carbohydrate content compared to a corresponding non-transgenic plant is described. In a first embodiment of the aspect a seed or plant tissue is obtained by the transgenic maize or sorghum plant.

In a twenty-third aspect, a method of identifying a drought and salinity resistant transgenic plant having one or more nucleotides encoding an AP2/ERF and/or NF-YB transcription factor, wherein the AP2/ERF transcription factor is encoded by the nucleotide sequence of SEQ ID NOs: 1 or 2 and the NF-YB transcription factor is encoded by the nucleotide sequence of SEQ ID NO: 3 or a ortholog, homolog, or functional fragment thereof comprising, (a) growing a population of transgenic and wild-type plants under conditions of drought and salinity stress; (b) selecting a transgenic plant that exhibits tolerance to drought and salinity, thereby identifying a transgenic plant that comprises a genotype associated with tolerance to drought and salinity is described.

BRIEF DESCRIPTION OF THE DRAWINGS

The foregoing will be apparent from the following more particular description of example embodiments of the invention, as illustrated in the accompanying drawings in which like reference characters refer to the same parts throughout the different views. The drawings are not necessarily to scale, emphasis instead being placed upon illustrating embodiments of the present invention.

FIG. 1 graphically illustrates the transcriptional regulatory network model of the switchgrass transcription factors PvSTR1, PvSTIF1 and PvBMY1 and their association to improved plant productivity and stress tolerance. The thick arrows illustrate the observed increased carbon flow directly regulated by the transcription factors, whereas the small arrows indicate the interactions with downstream TFs for regulation of key genes in major metabolic pathways.

FIG. 2 illustrates the tissue specific expression pattern of the transcription factor genes PvSTR1, PvSTIF1 and PvBMY1 in wild type switchgrass analyzed by RT-PCR. Total RNA was isolated from roots (R), young leaves (YL), culms (C), mature leaves (ML), leaf sheaths (LS), and/or panicles (P) of wild-type plants and subjected to reverse transcription and PCR using One Step RT-PCR Kit (Qiagen) and primers specific for the coding regions of the TF genes.

FIG. 3 demonstrates the presence of genes homologous to the transcription factor genes PvSTR1, PvSTIF1 and PvBMY1 in the switchgrass genome as detected by Southern blot hybridization. Genomic DNA isolation, digestion with EcoRI and hybridization with probes specific for the coding regions of the transcription factor genes was performed as described previously (Somleva et al., 2008, Plant Biotechnol J, 6: 663-678). 16 and 56, Alamo genotypes (our designation).

FIG. 4A-C shows the multiple sequence alignment for the conserved domains of PvSTR1 (FIG. 4A), PvSTIF1 (FIG. 4B) and PvBMY1 (FIG. 4C) in switchgrass (Panicum virgatum L.) and other plant species. The alignments of the DNA-binding domain sequences (AP2/ERF for STIF1 and STR1 and NFYB-HAP3 for BMY1) obtained using Clustal W program (Thompson et al., 1994, Nucleic Acids Res. 11: 4673-4680) are shown in the boxes.

FIG. 5A-C illustrates the possible phylogenetic relationships among the higher plant taxa, including monocotyledonous and dicotyledonous species, based on the conservative domains of PvSTR1 (A), PvSTIF1 (B) and PvBMY1 (C).

FIG. 6A-C shows the vectors pMBXS809 (A), pMBXS810 (B) and pMBXS855 (C) harboring the TF genes and the marker gene bar.

FIG. 7A-C depicts the vectors pMBXS881 (A), pMBXS882 (B) and pMBXS883 (C) harboring the TF genes and the marker gene hptII.

FIG. 8 shows results from qRT-PCR (quantitative reverse transcription polymerase chain reaction or real-time RT-PCR) analysis of the overexpression of the transcription factor genes PvSTR1 (A), PvSTIF1 (B) and PvBMY1 (C) in transgenic switchgrass plants prior to transfer to soil. β-actin amplification was used for transcript normalization. WT1, plants regenerated from non-transformed mature caryopsis-derived callus cultures from genotype 16; WT2, plants regenerated from non-transformed immature inflorescence-derived cultures from genotype 56; 1-5, transgenic lines representing independent transformation events. Data presented as mean values±SE (n=3).

FIG. 9 shows Western blots of total proteins from transgenic and wild-type switchgrass plants. A Protein extracts (6 μg per lane) from PvSTR1 and PvSTIF1 lines incubated with antibodies against the proteins of the light harvesting centers of photosystem I (LhcA3) and photosystem II (LhcB5). β-actin was used as a loading control. B Total protein extracts (6 μg per lane) from PvBMY1 lines incubated with an antibody against phosphoenolpyruvate carboxylase (PEPC). β-actin was used as a loading control. Protein isolation and membrane blotting were performed as described previously (Somleva et al., 2008, Plant Biotechnol J, 6: 663-678). Commercially available antibodies (Agrisera) were used for protein detection. An ultra-sensitive chemiluminescent substrate system (Thermo Scientific) was used for signal development. Lanes: WT—a control, wild-type plant; 1 to 4—transgenic switchgrass plants representing different TF lines.

FIG. 10 illustrates the effect of high salinity stress on relative water content (A), the abundance of the chloroplastic Cu—Zn superoxide dismutase (SOD) protein (B) and levels of photosynthetic pigments (C) in switchgrass plants overexpressing the PvSTR1 and PvSTIF1 genes. Bars represent mean±SD values (n=3).

FIG. 11 illustrates the large number of switchgrass genes, including transcription factors whose expression is impacted by over-expression of PvSTR1, PvSTIF1 and PvBMY1. The data is presented as the total number of regulated orthologs (A) as well as the numbers of up-regulated (B) and down-regulated (C) genes common for the three TFs.

FIG. 12 presents the gene ontology analysis of differentially expressed genes regulated by PvSTR1 (A), PvSTIF1 (B) and PvBMY1(C) transcription factors. Descriptions of biological functions were assigned on the basis of information retrieved from the world wide web at: bioinfo.cau.edu.cn/agriGO/index.php (P-value calculated by Fisher exact test). Genes that showed more than 2-fold up-regulation and the top enriched pathways are considered for the graphs.

DETAILED DESCRIPTION OF THE INVENTION

A description of example embodiments of the invention follows.

I. Definitions

Unless otherwise indicated, the disclosure encompasses all conventional techniques of plant transformation, plant breeding, microbiology, cell biology and recombinant DNA, which are within the skill of the art. See, e.g., Sambrook and Russell, Molecular Cloning: A Laboratory Manual, 3rd edition, 2001; Current Protocols in Molecular Biology, F. M. Ausubel et al. eds., 1987; Plant Breeding: Principles and Prospects, M. D. Hayward et al., 1993; Current Protocols in Protein Science, Coligan et al., eds., 1995, (John Wiley & Sons, Inc.); the series Methods in Enzymology (Academic Press, Inc.): PCR 2: A Practical Approach, M. J. MacPherson, B. D. Hames and G. R. Taylor eds., 1995.

Unless otherwise noted, technical terms are used according to conventional usage. Definitions of common terms in molecular biology may be found in Lewin, Genes VII, 2001 (Oxford University Press), The Encyclopedia of Molecular Biology, Kendrew et al., eds., 1999 (Wiley-Interscience) and Molecular Biology and Biotechnology, a Comprehensive Desk Reference, Robert A. Meyers, ed., 1995 (VCH Publishers, Inc), Current Protocols In Molecular Biology, F. M. Ausubel et al., eds., 1987 (Green Publishing), Sambrook and Russell, Molecular Cloning: A Laboratory Manual, 3rd edition, 2001.

A number of terms used herein are defined and clarified in the following section.

As used herein, a “vector” is a replicon, such as a plasmid, phage, or cosmid, into which another DNA segment may be inserted so as to bring about the replication of the inserted segment. The vectors described herein can be expression vectors.

As used herein, an “expression vector” is a vector that includes one or more expression control sequences.

As used herein, an “expression control sequence” is a DNA sequence that controls and regulates the transcription and/or translation of another DNA sequence.

As used herein, “operably linked” means incorporated into a genetic construct so that expression control sequences effectively control expression of a coding sequence of interest.

As used herein, “transformed” and “transfected” encompass the introduction of a nucleic acid (e.g., a vector) into a cell by a number of techniques known in the art.

“Plasmids” are designated by a lower case “p” preceded and/or followed by capital letters and/or numbers.

The term “plant” is used in its broadest sense. It includes, but is not limited to, any species of woody, ornamental or decorative, crop or cereal, fruit or vegetable plant, and photosynthetic green algae (e.g., Chlamydomonas reinhardtii). It also refers to a plurality of plant cells that is largely differentiated into a structure that is present at any stage of a plant's development. Such structures include, but are not limited to, a fruit, shoot, stem, leaf, flower petal, etc.

The term “plant tissue” includes differentiated and undifferentiated tissues of plants including those present in roots, shoots, leaves, inflorescences, anthers, pollen, ovaries, seeds and tumors, as well as cells in culture (e.g., single cells, protoplasts, embryos, callus, etc.). Plant tissue may be in planta, in organ culture, tissue culture, or cell culture.

The term “plant part” as used herein refers to a plant structure, a plant organ, or a plant tissue.

A “non-naturally occurring plant” refers to a plant that does not occur in nature without human intervention. Non-naturally occurring plants include transgenic plants, plants created through genetic engineering and plants produced by non-transgenic means such as traditional or market assisted plant breeding.

The term “plant cell” refers to a structural and physiological unit of a plant, comprising a protoplast and a cell wall. The plant cell may be in the form of an isolated single cell or a cultured cell, or as a part of a higher organized unit such as, for example, a plant tissue, a plant organ, or a whole plant.

The term “plant cell culture” refers to cultures of plant units such as, for example, protoplasts, cells and cell clusters in a liquid medium or on a solid medium, cells in plant tissues and organs, microspores and pollen, pollen tubes, anthers, ovules, embryo sacs, zygotes and embryos at various stages of development.

The term “plant material” refers to leaves, stems, roots, inflorescences and flowers or flower parts, fruits, pollen, anthers, egg cells, zygotes, seeds, cuttings, cell or tissue cultures, or any other part or product of a plant.

A “plant organ” refers to a distinct and visibly structured and differentiated part of a plant, such as a root, stem, leaf, flower bud, inflorescence, spikelet, floret, seed or embryo.

The term “non-transgenic plant” refers to a plant that has not been genetically engineered with heterologous nucleic acids. These non-transgenic plants can be the test or control plant when comparisons are made, including wild-type plants.

A “corresponding non-transgenic plant” refers to the plant prior to the introduction of heterologous nucleic acids. This plant can be the test plant or control plant, including wild type plants.

A “trait’ refers to morphological, physiological, biochemical and physical characteristics or other distinguishing feature of a plant or a plant part or a cell or plant material.

The term “trait modification” refers to a detectable change in a characteristic of a plant or a plant part or a plant cell induced by the expression of a polynucleotide or a polypeptide of the invention compared to a plant not expressing them, such as a wild type plant. Some trait modifications can be evaluated quantitatively, such as content of different metabolites, proteins, pigments, lignin, vitamins, starch, sucrose, glucose, fatty acids and other storage compounds, seed size and number, organ size and weight, total plant biomass and yield of genetically engineered products.

Trait modifications of further interest include those to seed (such as embryo or endosperm), fruit, root, flower, leaf, stem, shoot, seedling or the like, including: enhanced tolerance to environmental conditions including freezing, chilling, heat, drought, water saturation, radiation and ozone; improved growth under poor photoconditions (e.g., low light and/or short day length), or changes in expression levels of genes of interest. Other phenotype that can be modified relate to the production of plant metabolites, such as variations in the production of photosynthetic pigments, enhanced or compositionally altered protein or oil production (especially in seeds), or modified sugar (insoluble or soluble) and/or starch composition. Physical plant characteristics that can be modified include cell development (such as the number of trichomes), fruit and seed size and number, yields and size of plant parts such as stems, leaves and roots, the stability of the seeds during storage, characteristics of the seed pod (e.g., susceptibility to shattering), root hair length and quantity, internode distances, or the quality of seed coat. Plant growth characteristics that can be modified include growth rate, germination rate of seeds, vigor of plants and seedlings, leaf and flower senescence, male sterility, apomixis, flowering time, flower abscission, rate of nitrogen uptake, biomass or transpiration characteristics, as well as plant architecture characteristics such as apical dominance, branching patterns, number of organs, organ identity, organ shape or size.

As used herein “abiotic stress” includes but is not limited to stress caused by any one of the following: drought, salinity, extremes or atypical temperature, chemical toxicity and oxidative variation. The ability to improve plant tolerance to abiotic stress would be of great economic advantage to farmers worldwide and would allow for the cultivation of crops during adverse conditions and in territories where cultivation of crops may not otherwise be possible.

Methods and Transgenic Plants, Plant Tissue, Seed and Plant Cell of the Invention

Described herein are methods of producing a transgenic plant, plant tissue, seed, or plant cell, wherein said plant, plant tissue, seed or plant cell comprises incorporated in the genome of said plant, plant tissue, seed, or plant cell: a polynucleotide encoding a plant transcription factor together with sequences to enable its increased expression or regulatory sequences inserted to increase the expression of a heterologous plant transcription factor.

It was found that incorporation of transcription factors encoded by the nucleotides SEQ ID NOs: 1, 2, and 3 modified expression of certain genes in a transgenic plant and increased the carbon flow of the transgenic plant without the corresponding increase in biomass. For example, increases in the levels of non-structural carbohydrates such as starch, sucrose and glucose levels in a transgenic plant are found to be greater than 2 fold increase but without an increase in the biomass or an insignificant increase in the biomass compared to the increases in the non-structural carbohydrates.

II. Transcriptional Regulation of Gene Expression in Plants

Transcription factors (TFs) are known to be involved in various biological processes, acting as activators or repressors of other genes or gene families, suggesting the function of various transcriptional regulatory mechanisms in regulating downstream signal transduction pathways. The regulatory logic that drives any plant response is governed by the combination of signaling regulators, TFs, their binding site in the regulatory regions of target genes (cis-regulatory elements; CREs) and other regulatory molecules (e.g., chromatin modifiers and small RNAs), as well as protein and RNA degradation machinery (Krishnan & Pereira, 2008, Brief Funct. Genomic. Proteomic. 7: 264-74). TFs control the expression of many target genes through specific binding of the TF to the corresponding CRE in the promoters of respective target genes. For example, recent reports suggest that the maize Dof1 and MNF factors bind to the promoter of PEPC, an enzyme in the C₄ cycle of photosynthesis (reviewed in Weissmann & Brutnell, 2012, Current Opinion Biotech. 23: 298-304). Several TFs are known to be induced by stress, acting as activators or repressors, suggesting the function of various transcriptional regulatory mechanisms in regulating specific biological processes and or pathways.

Identification and Mapping Regulatory Domains of TFs:

Targeted gene regulation via designed transcription factors has great potential for precise phenotypic modification and acceleration of novel crop trait development. Over the past few years many transcription factors have been shown to contain regulatory domains, which can increase or decrease their transcriptional and/or DNA-binding activity. The mechanisms by which this regulation takes place frequently involve phosphorylation, dimer formation or interaction with negative or positive cofactors (Facchinetti et al., 1997, Biochem. J. 324: 729-736). Nevertheless, different organisms have evolved with diverse temporal and spatial regulation of transcription. In general, the temporal and spatial regulations are mediated by different classes of DNA binding transcriptional activator proteins. Unlike DNA binding domains, the transcription activation domains (TAD) have less primary amino acid sequence similarity. The TADs have been classified into acidic, glutamine-rich, proline-rich and serine/threonine-rich. We have identified putative transcription activation domains of the transcription factors of the invention based on the bioinformatics analysis.

Spatio-Temporal Gene Expression Through Novel cis-Regulatory Elements:

Spatio-temporal gene expression is the activation of genes within specific tissues of an organism at specific times during development. Plant promoters have attracted increasing attention because of their irreplaceable role in modulating the spatio-temporal expression of genes interacting with transcription factors (TFs). The control of gene expression is largely determined by cis-regulatory modules localized in the promoter sequence of regulated genes and their cognate transcription factors. While there has been a substantial progress in dissecting and predicting cis-regulatory activity, our understanding of how information from multiple enhancer elements converge to regulate a gene's expression remains elusive. Constitutive promoters are widely used to functionally characterize plant genes in transgenic plants but their lack of specificity and poor control over protein expression can be a major disadvantage. On the other hand, promoters that provide precise regulation of temporal or spatial transgene expression facilitate such studies by targeting overexpression or knockdown of target genes to specific tissues and/or at particular developmental stages. Promoter-based transgenic technologies have already been applied to a great effect in wheat, where a heat-inducible promoter in transgenic plants effectively controlled the spatio-temporal expression of a transgene (Freeman et al., 2011, Plant Biotech. J. 9: 788-796). A modular synthetic promoter for the spatio-temporal control of transgene expression in stomata has been reported by fusing a guard cell-specific element from the promoter of the potato phosphoenolpyruvate carboxylase (PEPC) gene with the ethanol-inducible gene switch AlcR/alcA (Xiong et al., 2009, J. Exp. Bot. 60: 4129-4136). Recently, a chimeric inducible system was developed, which combined the cellular specificity of the AtMYB60 minimal promoter with the positive responsiveness to dehydration and ABA of the rd29A promoter (Rusconi et al., 2013, J. Exp. Bot. 64: 3361-3371). Remarkably, the synthetic module specifically up-regulated gene expression in guard cells of Arabidopsis, tobacco, and tomato in response to dehydration or ABA. Likewise, promoter cloning and subsequent manipulation of spatio-temporal gene expression together with transcription activation domains from the switchgrass transcription factors described in the presented invention offers a significant promise in genetically engineering novel adaptive traits in biomass and bioenergy crops.

III. Plant Transformation Technologies

The transcription factor genes of this invention can be introduced into the genome of any plant by any of the methods for nuclear transformation known in the art. Methods for transformation of a range of plants useful for practicing the current invention are described in the examples herein. Any other genes of interest can be introduced into the genome and/or plastome of any plant by any of the methods for nuclear and plastid transformation known in the art. Other genes of interest can include herbicide resistance genes, pest resistance genes, fungal resistance genes, genes for enhancing oil yield or genes for novel metabolic pathways enabling the production of non-plant products to be made by the plant. The product of any transgene can be targeted to one or more of the plant cell organelles using any of the targeting sequences and methods known in the art.

A. Genetic Constructs for Transformation

DNA constructs useful in the methods described herein include transformation vectors capable of introducing transgenes into plants. As used herein, “transgenic” refers to an organism in which a nucleic acid fragment containing a heterologous nucleotide sequence has been introduced. The transgenes in the transgenic organism are preferably stable and inheritable. The heterologous nucleic acid fragment may or may not be integrated into the host genome.

Several plant transformation vector options are available, including those described in Gene Transfer to Plants, 1995, Potrykus et al., eds., Springer-Verlag Berlin Heidelberg New York, Transgenic Plants: A Production System for Industrial and Pharmaceutical Proteins, 1996, Owen et al., eds., John Wiley & Sons Ltd. England, and Methods in Plant Molecular Biology: A Laboratory Course Manual, 1995, Maliga et al., eds., Cold Spring Laboratory Press, New York. Plant transformation vectors generally include one or more coding sequences of interest under the transcriptional control of 5′ and 3′ regulatory sequences, including a promoter, a transcription termination and/or polyadenylation signal, and a selectable or screenable marker gene. For the expression of two or more polypeptides from a single transcript, additional RNA processing signals and ribozyme sequences can be engineered into the construct (U.S. Pat. No. 5,519,164). This approach has the advantage of locating multiple transgenes in a single locus, which is advantageous in subsequent plant breeding efforts.

Engineered minichromosomes can also be used to express one or more genes in plant cells. Cloned telomeric repeats introduced into cells may truncate the distal portion of a chromosome by the formation of a new telomere at the integration site. Using this method, a vector for gene transfer can be prepared by trimming off the arms of a natural plant chromosome and adding an insertion site for large inserts (Yu et al., 2006, Proc. Natl. Acad. Sci. USA 103: 17331-17336; Yu et al., 2007, Proc. Natl. Acad. Sci. USA 104: 8924-8929).

An alternative approach to chromosome engineering in plants involves in vivo assembly of autonomous plant minichromosomes (Carlson et al., 2007, PLoS Genet. 3: 1965-74). Plant cells can be transformed with centromeric sequences and screened for plants that have assembled autonomous chromosomes de novo. Useful constructs combine a selectable marker gene with genomic DNA fragments containing centromeric satellite and retroelement sequences and/or other repeats.

Another approach useful to the described invention is Engineered Trait Loci (“ETL”) technology (U.S. Pat. No. 6,077,697; US 2006/0143732). This system targets DNA to a heterochromatic region of plant chromosomes, such as the pericentric heterochromatin, in the short arm of acrocentric chromosomes. Targeting sequences may include ribosomal DNA (rDNA) or lambda phage DNA. The pericentric rDNA region supports stable insertion, low recombination, and high levels of gene expression. This technology is also useful for stacking of multiple traits in a plant (US 2006/0246586).

Zinc-finger nucleases (ZFNs) are also useful for practicing the invention in that they allow double strand DNA cleavage at specific sites in plant chromosomes such that targeted gene insertion or deletion can be performed (Shukla et al., 2009, Nature 459: 437-441; Townsend et al., 2009, Nature 459: 442-445). This approach may be particularly useful for the present invention which can involve transcription factor genes which are naturally present in the genome of the plant of interest. In this case the ZFNs can be used to change the sequences regulating the expression of the TF of interest to increase the expression or alter the timing of expression beyond that found in a non-engineered or wild type plant.

A transgene may be constructed to encode a multifunctional transcription factor combining different domains of the transcription factors identified herein as useful for practicing the claimed invention through gene fusion techniques in which the coding sequences of different domains of the different genes are fused with or without linker sequences to obtain a single gene encoding a single protein with the activities of the individual genes. Such synthetic fusion gene/TF combinations can be further optimized using molecular evolution technologies.

B. Tissue Culture-Based Methods for Nuclear Transformation

Transformation protocols as well as protocols for introducing nucleotide sequences into plants may vary depending on the type of plant or plant cell, i.e., monocot or dicot, targeted for transformation.

Suitable methods of introducing nucleotide sequences into plant cells and subsequent insertion into the plant genome are described in US 2010/0229256 A1 to Somleva & Ali and US 2012/0060413 to Somleva et al.

The transformed cells are grown into plants in accordance with conventional techniques. See, for example, McCormick et al., 1986, Plant Cell Rep. 5: 81-84. These plants may then be grown, and either pollinated with the same transformed variety or different varieties, and the resulting hybrid having constitutive expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that constitutive expression of the desired phenotypic characteristic is stably maintained and inherited and then seeds harvested to ensure constitutive expression of the desired phenotypic characteristic has been achieved.

C. In Planta Transformation Methods

Procedures for in planta transformation can be simple. Tissue culture manipulations and possible somaclonal variations are avoided and only a short time is required to obtain transgenic plants. However, the frequency of transformants in the progeny of such inoculated plants is relatively low and variable. At present, there are very few species that can be routinely transformed in the absence of a tissue culture-based regeneration system. Stable Arabidopsis transformants can be obtained by several in planta methods including vacuum infiltration (Clough & Bent, 1998, The Plant J. 16: 735-743), transformation of germinating seeds (Feldmann & Marks, 1987, Mol. Gen. Genet. 208: 1-9), floral dip (Clough and Bent, 1998, Plant J. 16: 735-743), and floral spray (Chung et al., 2000, Transgenic Res. 9: 471-476). Other plants that have successfully been transformed by in planta methods include rapeseed and radish (vacuum infiltration, Ian and Hong, 2001, Transgenic Res., 10: 363-371; Desfeux et al., 2000, Plant Physiol. 123: 895-904), Medicago truncatula (vacuum infiltration, Trieu et al., 2000, Plant J. 22: 531-541), camelina (floral dip, WO/2009/117555 to Nguyen et al.), and wheat (floral dip, Zale et al., 2009, Plant Cell Rep. 28: 903-913). In planta methods have also been used for transformation of germ cells in maize (pollen, Wang et al. 2001, Acta Botanica Sin., 43, 275-279; Zhang et al., 2005, Euphytica, 144, 11-22; pistils, Chumakov et al. 2006, Russian J. Genetics, 42, 893-897; Mamontova et al. 2010, Russian J. Genetics, 46, 501-504) and Sorghum (pollen, Wang et al. 2007, Biotechnol. Appl. Biochem., 48, 79-83)

D. Transformation of Plants with Genes of Interest

Transgenic plants can be produced using conventional techniques to express any genes of interest in plants or plant cells (Methods in Molecular Biology, 2005, vol. 286, Transgenic Plants: Methods and Protocols, Pena L., ed., Humana Press, Inc. Totowa, N.J.). Typically, gene transfer, or transformation, is carried out using explants capable of regeneration to produce complete, fertile plants. Generally, a DNA or an RNA molecule to be introduced into the organism is part of a transformation vector. A large number of such vector systems known in the art may be used, such as plasmids. The components of the expression system can be modified, e.g., to increase expression of the introduced nucleic acids. For example, truncated sequences, nucleotide substitutions or other modifications may be employed. Expression systems known in the art may be used to transform virtually any plant cell under suitable conditions. A transgene comprising a DNA molecule encoding a gene of interest is preferably stably transformed and integrated into the genome of the host cells. Transformed cells are preferably regenerated into whole plants. Detailed description of transformation techniques are within the knowledge of those skilled in the art.

1. Genes for Transcription Factors

Crop improvement using transcription factors (TFs) is a promising approach as they are likely to regulate a wide range of target genes whose products contribute to plant agronomic performance under normal and stress conditions. TF-mediated improvement of stress tolerance has been reported in diverse crop species, both dicots and monocots (Hussain et al., 2011, Biotechnology Prog. 27: 297-306). The first efforts included overexpression of the AP2/ERF factors CBF1, DREB1A and CBF4 that resulted in drought/salt/cold tolerance in Arabidopsis (Jaglo-Ottosen et al., 1998, Science 280: 104-106). Since then, the orthologous genes of CBF/DREB have been identified in many crop plants and functional tests revealed conservation of function (reviewed in Xu et al., 2011. J. Int. Plant Biol. 53: 570-585). It has also been shown that ectopic overexpression of these TF genes caused, in addition to increased stress tolerance, some specific phenotypic changes—dark-green, dwarfed plants with higher levels of soluble sugars and proline have been obtained. More recent evidence suggested the role of an AP2 family protein SHINE/WAX INDUCER 1 (SHN) as a global level regulator of cell wall biosynthesis which could be economically valuable for biofuel production from lignocellulosic crops (Ambavaram et al., 2011, Plant Physiol. 155: 916-931).

In studies with model plants, it has been shown that transcription factors belonging to the AP2/ERF, NF-Y, bZIP, MYB, Zinc-finger and NAC families confer tolerance to both biotic and abiotic stresses. Comparative genomics has also been used to find genes with conserved functions between model plants (mainly Arabidopsis) and crop plants, such as rice and maize demonstrating the utility of using the dicot-monocot models together. For example, expression of an Arabidopsis AP2/ERF-like transcription factor in rice resulted in an increase in leaf biomass and bundle sheath cells that probably contributed to the enhanced photosynthetic assimilation and efficiency (Karaba et al., 2009, Proc. Natl. Acad. Sci. USA 104: 15270-15275).

2. Reporter Genes and Selectable Marker Genes

Reporter genes or selectable marker genes may be included in an expression cassette as described in US Patent Applications 20100229256 and 20120060413 incorporated by reference herein. An expression cassette including a promoter sequence operably linked to a heterologous nucleotide sequence of interest can be used to transform any plant by any of the methods described above. Useful selectable marker genes and methods of selection transgenic lines for a range of different crop species are described in the examples herein.

E. Transgene Expression in Plants

Plant promoters can be selected to control the expression of the transgene in different plant tissues or organelles for all of which methods are known to those skilled in the art (Gasser & Fraley, 1989, Science 244: 1293-1299). In one embodiment, promoters are selected from those of eukaryotic or synthetic origin that are known to yield high levels of expression in plant and algae. In a preferred embodiment, promoters are selected from those that are known to provide high levels of expression in monocots.

1. Inducible Promoters

Chemical-regulated promoters can be used to modulate the expression of a gene in a plant through the application of an exogenous chemical regulator. Depending upon the objective, the promoter may be a chemical-inducible promoter, where application of the chemical induces gene expression, or a chemical-repressible promoter, where application of the chemical represses gene expression. Chemical-inducible promoters are known in the art and include, but are not limited to, the maize 1n2-2 promoter, which is activated by benzenesulfonamide herbicide safeners, the maize GST promoter, which is activated by hydrophobic electrophilic compounds that are used as pre-emergent herbicides, and the tobacco PR-1 promoter which is activated by salicylic acid. Other chemical-regulated promoters include steroid-responsive promoters [see, for example, the glucocorticoid-inducible promoter (Schena et al., 1991, Proc. Natl. Acad. Sci. USA 88: 10421-10425; McNellis et al., 1998, Plant J. 14: 247-257) and tetracycline-inducible and tetracycline-repressible promoters (see, for example, Gatz et al., 1991, Mol. Gen. Genet. 227: 229-237; U.S. Pat. Nos. 5,814,618 and 5,789,156, herein incorporated by reference in their entirety).

A three-component osmotically inducible expression system suitable for plant metabolic engineering has recently been reported (Feng et al., 2011, PLoS ONE 6: 1-9).

2. Constitutive Promoters

Constitutive promoters include, for example, the core promoter of the Rsyn7 promoter and other constitutive promoters disclosed in WO 99/43838 and U.S. Pat. No. 6,072,050, the core CaMV 35S promoter (Odell et al., 1985, Nature 313: 810-812), rice actin (McElroy et al., 1990, Plant Cell 2: 163-171), ubiquitin (Christensen et al., 1989, Plant Mol. Biol. 12: 619-632; Christensen et al., 1992, Plant Mol. Biol. 18: 675-689), pEMU (Last et al., 1991, Theor. Appl. Genet. 81: 581-588), MAS (Velten et al., 1984, EMBO J. 3: 2723-2730), and ALS promoter (U.S. Pat. No. 5,659,026). Other constitutive promoters are described in U.S. Pat. Nos. 5,608,149; 5,608,144; 5,604,121; 5,569,597; 5,466,785; 5,399,680; 5,268,463; and 5,608,142.

3. Weak Promoters

Where low level expression is desired, weak promoters may be used. Generally, the term “weak promoter” is intended to describe a promoter that drives expression of a coding sequence at a low level. Where a promoter is expressed at unacceptably high levels, portions of the promoter sequence can be deleted or modified to decrease expression levels. Such weak constitutive promoters include, for example, the core promoter of the Rsyn7 promoter (WO 99/43838 and U.S. Pat. No. 6,072,050).

4. Tissue Specific Promoters

“Tissue-preferred” promoters can be used to target gene expression within a particular tissue. Compared to chemically inducible systems, developmentally and spatially regulated stimuli are less dependent on penetration of external factors into plant sells. Tissue-preferred promoters include those described by Van Ex et al., 2009, Plant Cell Rep. 28: 1509-1520; Yamamoto et al., 1997, Plant J. 12: 255-265; Kawamata et al., 1997, Plant Cell Physiol. 38: 792-803; Hansen et al., 1997, Mol. Gen. Genet. 254: 337-343; Russell et al., 199), Transgenic Res. 6: 157-168; Rinehart et al., 1996, Plant Physiol. 112: 1331-1341; Van Camp et al., 1996, Plant Physiol. 112: 525-535; Canevascini et al., 1996, Plant Physiol. 112: 513-524; Yamamoto et al., 1994, Plant Cell Physiol. 35: 773-778; Lam, 1994, Results Probl. Cell Differ. 20: 181-196, Orozco et al., 1993, Plant Mol. Biol. 23: 1129-1138; Matsuoka et al., 1993, Proc. Natl. Acad. Sci. USA 90: 9586-9590, and Guevara-Garcia et al., 1993, Plant J. 4: 495-505. Such promoters can be modified, if necessary, for weak expression.

4.i. Seed/Embryo Specific Promoters

“Seed-preferred” promoters include both “seed-specific” promoters (those promoters active during seed development such as promoters of seed storage proteins) as well as “seed-germinating” promoters (those promoters active during seed germination). See Thompson et al., 1989, BioEssays 10: 108-113, herein incorporated by reference. Such seed-preferred promoters include, but are not limited to, Cim1 (cytokinin-induced message), cZ19B1 (maize 19 kDa zein), mi1ps (myo-inositol-1-phosphate synthase), and celA (cellulose synthase). Gamma-zein is a preferred endosperm-specific promoter. Glob-1 is a preferred embryo-specific promoter. For dicots, seed-specific promoters include, but are not limited to, bean β-phaseolin, napin, β-conglycinin, soybean lectin, cruciferin, and the like. For monocots, seed-specific promoters include, but are not limited to, maize 15 kDa zein, 22 kDa zein, 27 kDa zein, g-zein, waxy, shrunken 1, shrunken 2, and globulin 1. The stage specific developmental promoter of the late embryogenesis abundant protein gene LEA has successfully been used to drive a recombination system for excision-mediated expression of a lethal gene at late embryogenesis stages in the seed terminator technology (U.S. Pat. No. 5,723,765 to Oliver et al.).

4.ii. Leaf Specific Promoters

Leaf-specific promoters are known in the art. See, for example, WO/2011/041499 and U. S. Patent No. 2011/0179511 A1 to Thilmony et al.; Yamamoto et al., 1997, Plant J. 12: 255-265; Kwon et al., 1994, Plant Physiol. 105: 357-367; Yamamoto et al., 1994, Plant Cell Physiol. 35: 773-778; Gotor et al., 1993, Plant J. 3: 509-518; Orozco et al., 1993, Plant Mol. Biol. 23: 1129-1138, and Matsuoka et al., 1993, Proc. Natl. Acad. Sci. USA 90: 9586-9590.

4.iii. Temporal Specific Promoters

Also contemplated are temporal promoters that can be utilized during the developmental time frame, for example, switched on after plant reaches maturity in leaf to enhance carbon flow.

4iv. Anther/Pollen Specific Promoters

Numerous genes specifically expressed in anthers and/or pollen have been identified and their functions in pollen development and fertility have been characterized. The specificity of these genes has been found to be regulated mainly by their promoters at the transcription level (Ariizumi et al., 2002, Plant Cell Rep. 21: 90-96 and references therein). A large number of anther- and/or pollen-specific promoters and their key cis-elements from different plant species have been isolated and functionally analyzed.

4.v. Floral Specific Promoters

Floral-preferred promoters include, but are not limited to, CHS (Liu et al., 2011, Plant Cell Rep. 30: 2187-2194), OsMADS45 (Bai et al., 2008, Transgenic Res. 17: 1035-1043), PSC (Liu et al., 2008, Plant Cell Rep. 27: 995-1004), LEAFY, AGAMOUS, and AP1 (Van Ex et al., 2009, Plant Cell Rep. 28: 1509-1520), AP1 (Verweire et al., 2007, Plant Physiol. 145: 1220-1231), PtAGIP (Yang et al., 2011, Plant Mol. Biol. Rep. 29: 162-170), Lem1 (Somleva & Blechl, 2005, Cereal Res. Comm. 33: 665-671; Skadsen et al., 2002, Plant Mol. Biol. 45: 545-555), Lem2 (Abebe et al., 2005, Plant Biotechnol. J. 4: 35-44), AGL6 and AGL13 (Schauer et al., 2009, Plant 59: 987-1000).

4.vi. Combinations of Promoters

Certain embodiments use transgenic plants or plant cells having multi-gene expression constructs harboring more than one promoter. The promoters can be the same or different.

Any of the described promoters can be used to control the expression of one or more of the transcription factor genes of the invention, their homologs and/or orthologs as well as any other genes of interest in a defined spatiotemporal manner.

F. Requirements for Construction of Plant Expression Cassettes

Nucleic acid sequences intended for expression in transgenic plants are first assembled in expression cassettes behind a suitable promoter active in plants. The expression cassettes may also include any further sequences required or selected for the expression of the transgene. Such sequences include, but are not restricted to, transcription terminators, extraneous sequences to enhance expression such as introns, vital sequences, and sequences intended for the targeting of the gene product to specific organelles and cell compartments. These expression cassettes can then be transferred to the plant transformation vectors described infra. The following is a description of various components of typical expression cassettes.

1. Transcriptional Terminators

A variety of transcriptional terminators are available for use in expression cassettes. These are responsible for the termination of transcription beyond the transgene and the correct polyadenylation of the transcripts. Appropriate transcriptional terminators are those that are known to function in plants and include the CaMV 35S terminator, the tm1 terminator, the nopaline synthase terminator and the pea rbcS E9 terminator. These are used in both monocotyledonous and dicotyledonous plants.

2. Sequences for the Enhancement or Regulation of Expression

Numerous sequences have been found to enhance gene expression from within the transcriptional unit and these sequences can be used in conjunction with the genes to increase their expression in transgenic plants. For example, various intron sequences such as introns of the maize Adh1 gene have been shown to enhance expression, particularly in monocotyledonous cells. In addition, a number of non-translated leader sequences derived from viruses are also known to enhance expression, and these are particularly effective in dicotyledonous cells.

G. Coding Sequence Optimization

The coding sequence of the selected gene may be genetically engineered by altering the coding sequence for optimal expression in the crop species of interest. Methods for modifying coding sequences to achieve optimal expression in a particular crop species are well known (Perlak et al., 1991, Proc. Natl. Acad. Sci. USA 88: 3324 and Koziel et al., 1993, Biotechnology 11: 194-200).

H. Construction of Plant Transformation Vectors

Numerous vectors available for plant transformation are known to those of ordinary skill in the plant transformation arts. The genes pertinent to this disclosure can be used in conjunction with any such vectors. The choice of vector depends upon the selected transformation technique and the target species.

Many vectors are available for transformation using Agrobacterium tumefaciens. These typically carry at least one T-DNA sequence and include vectors such as pBIN19. Typical vectors suitable for Agrobacterium transformation include the binary vectors pCIB200 and pCIB2001, as well as the binary vector pCIB 10 and hygromycin selection derivatives thereof. (See, for example, U.S. Pat. No. 5,639,949).

Transformation without the use of Agrobacterium tumefaciens circumvents the requirement for T-DNA sequences in the chosen transformation vector and consequently vectors lacking these sequences are utilized in addition to vectors such as the ones described above which contain T-DNA sequences. The choice of vector for transformation techniques that do not rely on Agrobacterium depends largely on the preferred selection for the species being transformed. Typical vectors suitable for non-Agrobacterium transformation include pCIB3064, pSOG 19, and pSOG35. (See, for example, U.S. Pat. No. 5,639,949).

I. Transformation and Selection of Cultures and Plants

Plant cultures can be transformed and selected using one or more of the methods described above which are well known to those skilled in the art. In switchgrass, selection occurs by incubating the cultures on a callus growth medium containing bialaphos. In an alternative embodiment, selection can occur in the presence of hygromycin. Resistant calluses are then cultured on a regeneration medium (Somleva, 2006, Agrobacterium Protocols, Wang K., ed., Vol. 2, pp 65-74, Humana Press; Somleva et al., 2002, Crop Sci. 42: 2080-2087) containing the preferred selection agent. Examples of specific selectable markers and transgenic plant selection methods for a number of crop species are described in the examples herein.

EXAMPLES Example 1 Identification and Functional Characterization of Candidate Transcription Factor Genes Potentially Involved in Photosynthesis and Biomass Related Traits

The following approaches were used to identify and annotate potential switchgrass transcription factors (TFs):

A. Gene Prediction Based on Systems Biology Approach

A rice regulatory association network that has been developed based on genome wide expression profiles (Ambavaram et al., 2011, Plant Physiol. 155: 916-931) was used to identify switchgrass orthologs of TFs with predicted function in the regulation of genes involved in photosynthesis and biomass related traits. Publicly available databases were used to perform BlastN and BlastP reciprocal searches between the genomes of rice (a C₃ monocot; http://rice.plantbiology.msu.edu), maize (a monocot possessing the NADP-ME subtype of C₄ photosynthesis; found at world wide web maizesequence.org and switchgrass an NAD-ME C₄ monocot at phytozome.net/search.php?show=blast&org=Org_Pvirgatum to identify candidate genes for functional validation and experimental analysis. Comparisons of gene ontology (GO) terms from the molecular function category revealed the most obvious functions of DNA binding and transcriptional regulatory activity of the identified TFs.

Based on genome-wide orthologous prediction, candidate genes were retrieved from the corresponding websites and their percentage of identity was evaluated (TABLE 1).

TABLE 1 Candidate transcription factor genes. Rice gene Maize gene Switchgrass ortholog % identity E-value LOC_Os02g10480 GRMZM2G138349 Pavirv00027905m 87.75 1e−86 LOC_Os07g41580 GRMZM2G384528 Pavirv00029298m 94.83 4e−58 LOC_Os02g52670 GRMZM2G103085 Pavirv00031839m 78.00 3e−11 LOC_Os09g11480 EU942421 Pavirv00046166m 75.44 2e−13 LOC_Os03g09170 GRMZM2G113060 Pavirv00021049m 61.11 3e−37 LOC_Os02g32140 GRMZM2G016434 Pavirv00013751m 97.26 8e−27 LOC_Os09g29960 GRMZM2G089850 Pavirv00059600m 94.59 3e−17 LOC_Os11g06770 GRMZM2G544539 Pavirv00009307m 91.94 1e−19 LOC_Os04g52090 GRMZM2G068967 Pavirv00015875m 98.31 2e−21 LOC_Os04g55520 GRMZM2G119865 Pavirv00033364m 66.67 4e−18

B. Functional Annotation of Select Switchgrass TFs

According to the plant transcription factor database (see world wide web at planttfdb.cbi.edu.cn) and switchgrass genome (world wide web at phytozome.net), SEQ ID NO: 1 (Pavirv00046166m) and SEQ ID NO: 2 (Pavirv00013751m) are switchgrass transcription factors belonging to the APETALA2 (AP2)/ETHYLENE RESPONSE FACTOR (ERF) family and SEQ ID NO: 3 (Pavirv00029298m) is a switchgrass transcription factor from the Nuclear-Factor Y (NF-YB) family. The analysis of their protein sequences using a database of protein domains, families and functional sites (world wide web at expacy.org) revealed the characteristic AP2 domain (SEQ ID NO: 4 and SEQ ID NO: 5, underlined) and NFYA-HAP2 motif (SEQ ID NO: 6, underlined), respectively. Comparisons of gene ontology terms for the switchgrass genes SEQ ID NO: 1 and SEQ ID NO: 2 revealed the ‘transcription factor’ activity (GO: 0003700), whereas SEQ ID NO: 3 belongs to the MNFs based on its sequence-specific transcription regulator activity (GO: 00030528). According to the TF-function association network, these switchgrass orthologous TF genes may be associated with functions in “primary” carbon metabolism and several “cellular metabolic” processes.

C. Expression Analysis of Novel Transcription Factors in Switchgrass.

For validation of the bioinformatics findings, the tissue specific expression of the candidate TF genes (TABLE 1) in switchgrass was analyzed by RT-PCR. Total RNA was isolated from root (R), culm (C), leaf sheath (LS), young leaf (YL), mature leaf (ML), and panicle (P) tissues of wild type plants. After DNase treatment and column purification, total RNA (200 ng per reaction) was subjected to reverse transcription and PCR in a one-step RT-PCR assay (Qiagen) with gene-specific primers.

The results revealed the differences in the expression levels of the candidate TF genes (listed in TABLE 1) in young and mature leaves, roots, and stem tissues (culm, leaf sheath and panicle). Based on their expression patterns we identified three genes which were highly expressed in mature leaf and these, three genes (SEQ ID NO: 1, SEQ ID NO: 2, and SEQ ID NO: 3) were selected for overexpression and functional analysis in switchgrass. The highest transcript accumulation for these three genes was observed in mature leaves (FIG. 2). No expression of the selected AP2/ERF transcription factors (SEQ ID NO: 1 and SEQ ID NO: 2) was detected in roots under the experimental conditions, while transcripts of the switchgrass NF-Y gene (SEQ ID NO: 3) were present at different levels in all tissues analyzed (FIG. 2).

Based on the effects of these TFs on plant metabolism and phenotype (see Example 5), the genes and the encoded polypeptides were designated as PvSTR1 (STarch Regulator 1; SEQ ID NO: 1 and SEQ ID NO: 4), PvSTIF1 (STress Inducible Factor 1; SEQ ID NO: 2 and SEQ ID NO: 5), and PvBMY1 (BioMass Yield 1, SEQ ID NO: 3 and SEQ ID NO: 6).

D. Identification of Homologous Genes of PvSTR1, PvSTIF1 and PvBMY1 Transcription Factors:

The sequence homology search was performed by comparing the deduced amino acid sequences of PvSTR1, PvSTIF1 and PvBMY1 to a translated non-redundant nucleotide database found on the world wide web at blast.ncbi.nlm.nih.gov and phytozome.net using tBLASTN and to a protein database using BLASTP. Transcription factor genes that are homologous to the transcription factors of the invention will typically have a polypeptide sequence of their conserved domain or the entire coding region 80% or more identical to the SEQ ID NOs: 4-6. As used herein, a “homolog” means a protein that performs the same biological function as another protein including these identified by sequence identity search. In silico analysis resulted in the identification of several homologs of each of the three transcription factors of the invention indicated as PvSTR2-5 (SEQ ID NOs: 7-10), PvSTIF2-4 (SEQ ID NOs: 11-13), and PvBMY2-6 (SEQ ID NOs: 14-18) for the homologs of PvSTR1, PvSTIF1 and PvBMY1, respectively.

The copy number of each of the TF genes in the switchgrass genome was also determined by Southern blot hybridizations. Two genotypes from the switchgrass cultivar Alamo-56 and 16 (our designation) were studied. Callus cultures from these genotypes were used in all the experiments on switchgrass transformation (as described in Example 3). The results revealed the presence of the same number of homologs of PvSTR1, PvSTIF1 and PvBMY1 in the two genotypes analyzed (FIG. 3).

Based on the existing sequential similarity, including the presence of identical DNA-binding domains, overexpression of the identified homologous genes PvSTR2-5, PvSTIF2-4, and PvBMY2-6 can readily be tested for trait modifications similar to the ones induced by PvSTR1, PvSTIF1 and PvBMY1.

E. Identification of Orthologous Genes of PvSTR1, PvSTIF1 and PvBMY1 Transcription Factors:

“Orthologs” and “paralogs” refer to polynucleotide and polypeptide sequences which are homologous to the claimed sequences. These genes are related because they originate from a common ancestral gene and potentially retain a similar function in the course of evolution. Orthologs are structurally related genes in different species that are derived by speciation, while paralogs are structurally related genes in the same species that are derived by genetic duplication. Orthologous genes are identified based upon percentage similarity or identity of the complete sequence or of a conserved domain. Closely related transcription factors can share about 70%, 75%, or about 80% or more amino acid sequence identity. Sequences with sufficient similarity may also bind to the same DNA binding sites of transcriptional regulatory elements.

Orthologs of the switchgrass transcription factor genes PvSTR1, PvSTIF1 and PvBMY1 were identified using methods well known in the art. Orthologous polypeptide sequences from different plant species with more than 75%, 80%, 85%, greater than 90% identity of the conserved binding domains are shown in FIG. 4. The phylogenetic relationships were also estimated based on the conserved domain sequences of PvSTR1, PvSTIF1 and PvBMY1 (FIG. 5).

Example 2 Design and Construction of Transformation Vectors for Overexpression of Transcription Factor Genes in Switchgrass.

All gene constructs were made using widely available genetic components and standard molecular biology techniques. Each of the genes was cloned in an individual expression cassette and 2-5 cassettes were assembled in one vector for plant transformation.

Two sets of gene constructs, one set containing the bar gene (conferring resistance to bialaphos) as a selectable marker and another one with the hptII gene (conferring resistance to hygromycin), were created for overexpression of the transcription factor genes of the invention in switchgrass (TABLE 2, FIG. 6, FIG. 7).

TABLE 2 Summary of plant transformation vectors for expression of transcription factors and PHB biosynthesis genes. Gene of Marker Vector Locus Name interest¹ gene² pMBXS809 Pavirv00046166m PvSTR1 bar pMBXS810 Pavirv00013751m PvSTIF1 bar pMBXS855 Pavirv00029298m PvBMY1 bar pMBXS881 Pavirv00046166m PvSTR1 hptII pMBXS882 Pavirv00013751m PvSTIF1 hptII pMBXS883 Pavirv00029298m PvBMY1 hptII ¹Driven by the maize cab-m5 promoter fused to the maize hsp70 intron; ²Driven by the 35S promoter.

The vectors pMBXS809, pMBXS810, and pMBXS855 (FIG. 6) were used for Agrobacterium-mediated transformation of switchgrass for generation of transgenic lines for functional analyses of the novel transcription factors (see Example 3). In each vector, the transcription factor gene is under the control of the cab-m5 light-inducible promoter of the chlorophyll a/b-binding protein in maize (Sullivan et al., 1989, Mol. Gen. Genet. 215: 431-440; Becker et al., 1992, Plant Mol. Biol. 20: 49-60) fused to the heat shock protein 70 (hsp70) intron (U.S. Pat. No. 5,593,874), while the marker genes are driven by the 35S promoter (TABLE 2).

The annotation of the genes and genetic elements assembled in the vectors pMBXS809, pMBXS810, and pMBXS855 are presented in TABLE 3 (see also FIG. 6 and FIG. 7).

TABLE 3 Plant transformation vectors for overexpression of the transcription factor genes PvSTR1, PvSTIF1 and PvBMY1 in switchgrass. Vector ID* TF gene/marker Annotation SEQ ID Coordinates (bp) pMBXS809 PvSTR1/bar Agrobacterium T-DNA right border 19  1 to 26 Cab-m5 promoter with hsp70  8951 to 10645 intron to drive PvSTR1 gene PvSTR1 coding region 10646 to 11636 nos terminator 11637 to 11891 CaMV35S promoter to drive bar gene 7911 to 8680 bar coding region 6543 to 7094 CaMV35S polyA terminator 6335 to 6537 Agrobacterium T-DNA left border 6260 to 6285 pMBXS810 PvSTIF1/bar Agrobacterium T-DNA right border 20  1 to 26 Cab-m5 promoter with hsp70  8951 to 10645 intron to drive PvSTIF1 gene PvSTIF1 coding region 10646 to 11240 nos terminator 11241 to 11495 CaMV35S promoter to drive bar gene 7911 to 8680 bar coding region 6543 to 7094 CaMV35S polyA terminator 6335 to 6537 Agrobacterium T-DNA left border 6260 to 6285 pMBXS855 PvBMY1/bar Agrobacterium T-DNA right border 21  1 to 26 Cab-m5 promoter with hsp70  8951 to 10645 intron to drive PvBMY1 gene PvBMY1 coding region 10646 to 11961 nos terminator 11978 to 12232 CaMV35S promoter to drive 7911 to 8680 bar gene bar coding region 6543 to 7094 CaMV35S polyA terminator 6335 to 6537 Agrobacterium T-DNA left border 6260 to 6285 *All vectors are based on the transformation vector pCambia3300 found at world wide web at cambia.org; the bar gene (conferring resistance to bialaphos) is used as a marker for selection of transformed callus cultures and plants.

Example 3 Transformation of Switchgrass

Highly embryogenic callus cultures initiated from different explants were used for introduction of the gene constructs described in Example 2.

Culture Initiation and Plant Regeneration:

Callus cultures were initiated from mature caryopses of cv. Alamo following a previously published procedure (Denchev & Conger, 1994, Crop Sci., 34: 1623-1627). Their embryogenic potential and plant regeneration ability were evaluated as described previously (U.S. Pat. No. 8,487,159 to Somleva et al.).

Switchgrass plants from Alamo genotype 56 (Somleva et al., 2008, Plant Biotechnol. J. 6: 663-678; U.S. Pat. No. 8,487,159 to Somleva et al.) grown under greenhouse conditions were used for initiation of immature inflorescence-derived callus cultures. The top culm nodes of elongating tillers with 3-4 visible nodes were used for development of inflorescences in tissue culture following a previously published procedure (Alexandrova et al., 1996, Crop Sci. 36: 175-178). Callus cultures were initiated from individual spikelets from in vitro developed panicles and propagated by transferring on to a fresh medium for callus growth (Denchev and Conger, 1994, Crop Sci. 34: 1623-1627) every four weeks.

Callus cultures were grown at 27° C., in the dark and maintained by monthly subcultures on a fresh medium for callus growth (Somleva et al., 2002, Crop Sci. 42: 2080-2087). For plant regeneration, calluses were plated on MS basal medium supplemented with 1.4 μM gibberellic acid and incubated at 27° C. with a 16-h photoperiod (cool white fluorescent bulbs, 80 μmol/m²/s).

Transformation of Mature Caryopsis—and Immature Inflorescence-Derived Cultures:

Highly embryogenic callus cultures were transformed with Agrobacterium tumefaciens following previously published protocols (Somleva et al., 2002, Crop Sci. 42: 2080-2087; Somleva, 2006, Agrobacterium Protocols, Wang K., ed., pp 65-74: Humana Press). Transformed cultures and plants regenerated from them were selected with 200 mg/L hygromycin (WO 2010/102220 A1 and US 2010/0229256 A1 to Somleva & Ali) or 10 mg/L bialaphos (Somleva et al., 2002, Crop Sci. 42: 2080-2087; Somleva, 2006, Agrobacterium Protocols, Wang K., ed., pp 65-74: Humana Press). Transgenic plants overexpressing the transcription factor genes PvSTR1, PvSTIF1, and PvBMY1 were obtained from cultures transformed with the vectors pMBXS809, pMBXS810, and pMBXS855 (TABLE 2). The presence of the transcription factor and marker genes in putative transformants was confirmed by PCR using primers specific for the coding regions of the transgenes and the amplification conditions described previously (Somleva et al., Plant Biotechnol. J. 6: 663-678). More than 200 T₀ plants representing 58 independent transformation events were identified (TABLE 4). Plants regenerated from untransformed callus cultures and grown under the same conditions were used as controls (non-transgenic plants; wild-type plants) in expression and functional analyses of transgenic lines.

TABLE 4 Transformations for overexpression of transcription factors in switchgrass. Gene of Alamo genotype 56¹ Alamo genotype 16² Vector interest # events³ # plants⁴ # events³ # plants⁴ pMBXS809 PvSTR1 8 60 6 31 pMBXS810 PvSTIF1 14 44 12 60 pMBXS855 PvBMY1 9 27 9 14 Total: 31 111 27 105 ¹immature inflorescence-derived callus cultures from this genotype were transformed; ²mature caryopsis-derived callus cultures from this genotype were transformed; ³number of bialaphos-resistant callus lines producing at least one transgenic plant; ⁴number of primary transformants (as confirmed by PCR).

After transfer to soil, transgenic and wild-type plants obtained from different transformation experiments were grown in a greenhouse at 27° C./24° C. (day/night) with supplemental lighting (16-h photoperiod, sodium halide lamps).

Example 4 Expression Analyses of Transgenic Switchgrass Plants Transformed with the Genes Encoding the Transcription Factors PvSTR1, PvSTIF1, and PvBMY1

In all experiments, total RNA was isolated from the second youngest leaf of primary transformants and control wild-type plants (3 plants per line) prior to transfer to soil using RNeasy Plant Mini Kit (Qiagen). After DNase treatment and column purification, different amounts of RNA were used for RT-PCR and qRT-PCR (quantitative reverse transcription polymerase chain reaction or real-time RT-PCR). Quantitative analysis of the differences in the expression levels of the TF genes in transgenic and control lines was performed by qRT-PCR using β-actin as a reference. For each sample, 500 ng of total RNA was converted into cDNA using iScript cDNA synthesis kit (Bio-Rad). The cDNA was diluted and subjected to real-time PCR using Fast SYBR® Green Master Mix (Life Technologies) in an Applied Biosystems 7500 Fast Real-Time PCR system. The amplification curves for each line were generated and used to calculate the relative expression ratio (fold change) compared to the wild type control. All of the transgenic lines analyzed showed significantly higher levels of expression of the transcription factor genes in the transgenic lines as compared to the control plants transcript accumulation (from 3 to 9.5 times higher as shown in FIG. 8).

Example 5 Effects of the Overexpression of the Transcription Factors PvSTR1, PvSTIF1 and PvBMY1 on Biomass Production and Photosynthetic Activity in Transgenic Switchgrass Plants

For functional characterization of PvSTR1, PvSTIF1 and PvBMY1 transcription factors, biochemical and physiological analyses were performed with transgenic and control wild-type switchgrass plants grown in soil for two months. Both groups of plants were from two Alamo genotypes—56 and 16 (our designation) differing in their morphology.

Measurements of Photosynthetic Activity:

For analyses of the photosynthesis rate in plants overexpressing the TF genes of the invention, various parameters were measured in light adapted leaves using a Dual-PAM-100 Measuring System (Heinz Walz GmbH). All measurements were performed with the leaf attached to the second node from the base of vegetative tillers with the forth emerging leaf.

The functioning of photosystem I (PSI) and photosystem II (PSII) was studied in terms of photochemical quantum yield (Y) and electron transport rate (ETR). Transgenic lines with improved photosynthetic capacity compared to wild type controls from the corresponding genotypes were identified (results are summarized in TABLE 5 for PvSTR1, PvSTIF1 and PvBMY1 lines, respectively). In some of the transgenic plants analyzed, the quantum yield of PSI and PSII were significantly increased at photosynthetically active radiation (PAR) of 30-37 μmol m⁻² s⁻¹ (TABLE 5). The electron transport rates of PSI and PSII in some of the transgenic plants were significantly elevated compared to the wild type control plants at PAR≥119 μmol m⁻² s⁻¹ (TABLE 5).

TABLE 5 Effect of the overexpression of transcription factors on photosynthesis. Y(I) Y(II) ETR(I) ETR(II) Max % to Max % to Max % to Max % to TF gene value¹ control² value¹ control² value¹ control² value¹ control² PvSTR1 0.802 137 0.735 112 46.8 131 12.2 130 PvSTIF1 0.746 125 0.714 108 49.7 139 12.8 136 PvBMY1 0.887 148 0.722 110 48.5 136 13.2 140 ¹The maximum value measured in individual transgenic switchgrass plants; ²Compared to the average values (5-6 plants, 2-3 measurements per plant) measured in the corresponding wild-type controls in terms of genotype, growth period and sampling date; Abbreviations: Y(I), photochemical quantum yield of photosystem I (PSI) - reflects the efficiency of quantum energy absorption by PSI reaction centers; Y(II), effective quantum yield of photosystem II (PSII) - represents the portion (from 0 to 1) of absorbed quanta that is converted into chemically fixed energy by the PSII reaction centers (the other portion of the quanta is dissipated into heat and fluorescence); ETR(I), electron transport rate of PSI - represents the rate of the cyclic or non-cyclic transfer of electrons from the excited reaction-center chlorophyll a molecule to the electron acceptor(s); ETR(II), electron transport rate of PSII - reflects the efficiency of the non-cyclic electron transfer.

Because of the linear correlation between the quantum yield of PSII and CO₂ fixation in C₄ plants (Leipner et al., 1999, Environ. Exp. Bot. 42: 129-139; Krall & Edwards, 1992, Physiol. Plant. 86: 180-187), the data suggested that the overexpression of the transcription factors resulted in improvement of the overall rate of photosynthesis (TABLE 5). This suggestion was supported by the significant increase in the electron transport rate (TABLE 5) based on the linear correlation between photosynthesis rate and ETR due to the lack of photorespiration in C₄ species (Kakani et al., 2008, Photosynthetica 46: 420-430). In addition, the enhanced ETR of PSI in some of the transgenic lines (TABLE 5) could indicate increased cyclic electron transport around PSI which provides the additional ATP needed for the CO₂ fixation cycle of the C₄ photosynthesis (Kiirats et al. 2010, Photosynth. Res. 105: 89-99).

After measurements of the photosynthetic activity, the leaf blades were sampled and used for determination of the contents of primary metabolites and photosynthetic pigments as well as for RNA and protein isolation.

Primary Metabolites:

Leaf tissue was ground in liquid nitrogen and freeze-dried for 3 days. Resultant leaf powder was used for measurements of the levels of primary metabolites using different analytical methods: a quantitative, enzymatic assay for starch (Starch Assay Kit, Sigma) and HPLC for soluble sugars and fatty acids.

The levels of products of the central carbon metabolism (starch, sucrose, glucose, and fatty acids) were measured in more than 80 transgenic plants representing 30 independent lines (10 lines/TF gene). The results are summarized in TABLE 6.

Photosynthetic Pigments:

Chlorophyll a, chlorophyll b, and carotenoids were determined in freshly harvested leaf tissue following a previously described procedure (Lichtenhaler, 1987, Methods Enzymol., 148: 350-382). The experiments were performed with 97 transgenic plants representing 30 independent lines (10 lines/TF gene). The results are summarized in TABLE 6.

This initial screening resulted in the identification of transgenic lines (2-5 plants per line) accumulating primary metabolites and pigments at levels significantly higher than the control untransformed plants grown under the same conditions. The data confirmed the predicted function of the tested TF genes as global regulators of the central carbon metabolism (see Example 1) and correlated with the results from the gene expression microarray analysis (see Example 7).

TABLE 6 Summary of the results from screening of transgenic switchgrass lines overexpressing the TF genes PvSTR1, PvSTIF1, and PvBMY1. Metabolites Biomass Soluble Fatty Pigments Dry No. of TF gene Line ID Starch sugars acids Chlorophyll Carotenoids weight tillers PvSTR1 56-1 128 101 123 144 133 132 118 56-2 125 97 111 137 125 112 111 56-3 123 156 107 88 79 102  95 56-7 160 138 117 144 141 139 131 56-9 159 120 115 116 111 140 128  56-13 152 125 107 201 181 143 152  56-14 339 244 80 109 100 113 112 16-4 n.a. n.a. 85 93 80  91 114 16-5 113 129 89 104 78 n.a. n.a. 16-6 168 115 90 119 124 103 111 PvSTIF1 56-2 180 93 130 142 129  94  68 56-3 104 123 128 136 121 105 108 56-4 n.a. 86 128 158 134  98 107 56-8 223 73 122 163 141 107 102 16-1 184 119 91 136 142 131 120 16-2 222 101 84 135 134 116 112 16-3 134 105 89 115 126 n.a. n.a. 16-4 153 114 88 131 132 137 129 16-6 201 88 90 125 139 142 138 16-9 186 117 101 125 139 111 126 PvBMY1 56-1  97 96 106 113 113 120 149 56-4 174 100 n.a. 106 84 115 142 56-6 136 137 94 112 98 123 135 56-7 123 127 110 117 117 123 156 56-8 141 152 99 103 101 133 148 56-9 223 192 104 80 73 124 158 16-1 n.a. 104 71 79 n.a. n.a. n.a. 16-2 126 99 106 111 111 124 194 16-3 270 158 75 92 91 n.a.  79 16-5 109 71 81 103 122  99  88 Values are average from measurements of 2-5 plants per transgenic line or wild type and are presented as % to the corresponding wild-type control in terms of genotype, growth period and sampling date; n.a.—not analyzed.

Individual plants with significantly higher levels of starch (4.2-fold increase), sucrose (4.4-fold increase), glucose (2.7-fold increase), fatty acids (1.5-fold increase), and total chlorophyll (2.5-fold increase) were identified (TABLE 7).

TABLE 7 Effect of the overexpression of transcription factors on the levels of primary metabolites and photosynthetic pigments in switchgrass leaves. Metabolite/ No. of plants Max value % to TF gene Pigment analyzed measured¹ control² Starch 26 11.659 405 PvSTR1 Sucrose 27 5.150 331 Glucose 27 0.575 192 (10 lines; Total fatty acids 19 4.065 148 30 plants Chlorophyll a + b 28 2.337 203 in total) Carotenoids 28 0.335 187 Starch 38 5.558 415 PvSTIF1 Sucrose 38 2.681 165 Glucose 38 0.735 269 (10 lines; Total fatty acids 32 4.159 150 41 plants Chlorophyll a + b 39 2.960 252 in total) Carotenoids 39 0.359 199 Starch 29 12.272 426 PvBMY1 Sucrose 27 6.768 435 Glucose 27 0.432 132 (10 lines; Total fatty acids 23 3.916 143 31 plants Chlorophyll a + b 30 1.589 135 in total) Carotenoids 30 0.259 144 ¹Data for starch, sucrose, glucose and fatty acids presented as % DW; data for chlorophyll a + b and carotenoids presented as mg/g FW; ²Values compared to the corresponding wild-type control in terms of genotype, growth period and sampling date.

A similar increase in the levels of primary metabolites was also detected in other plant parts. For example, the starch content in the second leaf of a plant from line 56-14 was 405% to the control (TABLE 6 and TABLE 7). The third and flag leaves from this plant also contained 4 times more starch than the corresponding leaves from wild-type control plants.

Unexpectedly, some of the transgenic switchgrass plants with significantly increased levels of starch and soluble sugars produced the same or slightly higher amounts of biomass compared to the control plants. For example, a plant from the PvBMY1 line 56-8 (TABLE 6) contained 3.2× more starch and 2.2× more sucrose and glucose than the corresponding control plants but its biomass was only 1% higher than the average biomass of the wild type plants. The total biomass yield of the plant with the highest starch content (415% to control) among the PvSTIF1 plants was similar to the biomass of the control wild-type plants. A 20% increase in biomass production was measured in a plant from the PvSTR1 line 56-14 (TABLE 6) despite the fact that the content of starch and soluble sugars in the leaves of this plant was 333% to the control.

Protein Analyses:

Western blot analysis of total proteins was performed as described previously (Somleva et al., 2008, Plant Biotechnol. J. 6: 663-678). An increase in the abundance of the proteins of the light harvesting centers of PSI (LhcA proteins) and PSII (LhcB proteins) was detected in most of the PvSTR1 and PvSTIF1 lines analyzed compared to the corresponding wild-type control (examples for LhcA3 and LhcB5 are shown in FIG. 9A). These findings are in agreement with the enhanced chlorophyll content in these lines (TABLE 6 and TABLE 7). The accumulation of phosphoenolpyruvate (PEPC) protein in most of the PvBMY1 lines was higher than in the wild-type plants (an example is shown in FIG. 9B).

This is the first report on the effect of any transcription factor on the abundance of Lhc and PEPC proteins.

Biomass Accumulation and Plant Development:

The growth and development of transgenic switchgrass plants overexpressing the transcription factors of the invention were monitored in terms of plant height and number of tillers after transfer to soil. All of the transgenic plants had larger leaf blades and longer internodes compared to the wild type plants from the corresponding genotype.

Total biomass yield was evaluated in plants grown under greenhouse conditions for five months as described in publications, WO 2012/037324 A2 and US 2012/0060413 to Metabolix. All vegetative and reproductive tillers at different developmental stages from each plant were counted and cut below the basal node. Leaves and stem tissues were separated, cut into smaller pieces, air-dried at 27° C. for 12-14 days and dry weight measurements were obtained. The number and ratio of vegetative to reproductive tillers were evaluated to compare the developmental patterns of transgenic and control plants.

The total biomass of 82 transgenic plants representing 29 TF lines and 12 wild type plants was measured. Transgenic lines with increased biomass yield (up to 142% to the control) and number of tillers (up to 194% to the control) were obtained (TABLE 6).

Most of the transgenic plants—81.5% of the analyzed PvSTR1 plants, 66.7% of the PvSTIF1 plants, and 82.1% of the PvBMY1 plants had higher biomass yield (up to 162%) compared to the control plants (TABLE 8). TF-overexpressing plants with significantly increased number of tillers (up to 216% to the control) were also identified.

TABLE 8 Effect of the overexpression of transcription factors on switchgrass biomass production. Max value % to TF gene Biomass measured [g DW] control¹ PvSTR1 Total 90.6 162 (10 lines; Leaves 25.9 149 27 plants Stem 71.4 184 analyzed) No. of tillers² 45 190 PvSTIF1 Total 70.9 153 (10 lines; Leaves 17.5 162 27 plants Stem 53.4 150 analyzed) No. of tillers² 25 166 PvBMY1 Total 79.6 142 (9 lines; Leaves 25.2 145 28 plants Stem 56.8 146 analyzed) No. of tillers² 51 216 ¹Values compared to the corresponding wild-type control in terms of genotype, growth period and sampling date; ²Total number of vegetative and reproductive tillers at different developmental stages (emerging tillers not included).

Similar patterns in the biomass productivity were observed in plants grown in soil for six months after repotting. For example, a plant from line 16-6 whose biomass was 148.8% to the control 4 months after transfer to soil yielded about 300 g DW total biomass after repotting which was 182.3% to the corresponding control.

Example 6 Evaluation of the Stress Response of Switchgrass Lines Overexpressing Transcription Factors

To validate the role of the transcription factors of the invention in improvement of plant stress tolerance, a novel method for screening of large populations of transgenic and control plants for their response to drought and salinity has been developed. It utilizes the previously developed tissue culture-based technology for propagation and improvement of polymer production in transgenic switchgrass plants (WO 2010/102220 A1 and US 2010/0229256 A1 to Somleva and Ali).

The stress-inducing conditions were established using non-transformed, wild-type plants. Polyethylene glycol (PEG) and NaCl were chosen for induction of drought and salinity stresses, respectively. Hundreds of plants were regenerated from immature inflorescence-derived callus cultures from Alamo genotype 56. After 3-4 weeks culture on MS medium for plant regeneration, phenotypically uniform plants were transferred to larger tissue culture containers containing the same medium supplemented with different concentrations of PEG and NaCl. Since the first stress-induced changes in plant morphology, such as leaf wilting and yellowing were observed after 3-4 days of treatment in preliminary experiments, this time period was used in the subsequent experiments. The relative water content (RWC), levels of photosynthetic pigments and abundance of the chloroplastic Cu—Zn superoxide dismutase (SOD) protein were used as stress markers. They were measured as follows: RWC according to Smart & Bingham, 1974, Plant Physiol. 53: 258-260, pigments as described by Lichtenhaler, 1987, Methods Enzymol., 148: 350-382 and SOD using a Plant SOD ELISA kit (MyBioSource).

Three different concentrations of the stress inducing agents were tested in 3 replicates each (10 plants/replicate). Based on the results from these treatments, 200 mM NaCl and 15% PEG were used in the experiments with the TF plants.

Plants regenerated from immature inflorescence-derived callus cultures initiated from well characterized TF lines along with wild type plants (regenerated from non-transformed cultures) were subjected to stress-inducing treatments under the conditions described above. Non-treated transgenic and wild type plants served as controls. All treatments were conducted in 3-4 replicates (10 plants per replicate).

As shown in the example in FIG. 10, treatment with 200 mM NaCl resulted in a slight decrease in RWC in the transgenic plants—2.2% and 1.6% in PvSTR1 and PvSTIF1 plants, respectively, while RWC in the wild-type plants was reduced with 7.6% compared to the non-treated control (FIG. 10A). Interestingly, RWC in the non-stressed TF plants was 4-8% higher than the relative water content in the wild type plants. Non-treated transgenic plants contained significantly lower amounts of the chloroplastic Cu—Zn superoxide dismutase (SOD) protein (as determined by ELISA) compared to non-stressed wild-type plants (FIG. 10B). High salinity stress conditions induced a similar increase in SOD levels in the PvSTIF1 and wild-type plants (16% and 19%, respectively) while the SOD protein content detected in the PvSTR1 plants was with about 7% higher than in the non-treated control (FIG. 10B). The non-treated TF plants also contained higher levels of photosynthetic pigments—27% and 43% higher total chlorophyll content in PvSTR1 and PvSTIF1 plants, respectively, compared to the unstressed wild type plants (FIG. 10C). The salinity stress caused a significant decrease (37-63%) in the chlorophyll content in both transgenic and wild type plants. The content of carotenoids in the stressed wild type plants was reduced with 18.2% compared to the non-treated plants, while in the TF plants it was 30-39% lower than in the corresponding control plants (FIG. 10C). Similar changes in the stress markers were observed when the plants were subjected to PEG-induced drought stress.

This is the first report demonstrating the effect of the overexpression of the transcription factors of the invention on plant stress response and the possibility to test the role of any transcription factors in this process under in vitro conditions.

Example 7 Global Gene Expression Analysis of Switchgrass Transgenic Lines Overexpressing PvSTR1, PvSTIF1 and PvBMY1

To identify the genes whose regulation by the transcription factors of the invention resulted in the observed improved biomass yield and stress tolerance (Examples 5 and 6), gene expression profiling was performed using an Affymetrix switchgrass cDNA GeneChip.

Gene expression microarrays, data processing and normalization: Three of the best performing switchgrass lines overexpressing one of the TF genes (TABLES 6-8) were selected for the microarray gene expression analysis. Total RNA was isolated from the second leaf of vegetative tillers (3-4 tillers per plant) as described in Example 3. RNA extracts from three plants from each line were pooled and their quality was evaluated using RNA Nano Chip (Agilent Technologies) according to the manufacturer's instructions. The microarray analysis was conducted using an Affymetrix switchgrass GeneChip containing probes to query approximately 43,344 transcripts following the manufacturer's protocol (http://www.affymetrix.com). Raw numeric values representing the signal of each feature were imported into AffylmGUI and the data were background corrected, normalized, and summarized using Robust Multiarray Averaging (RMA). A linear model was used to average data between the replicates and to detect differential expression. Data quality was assessed using box and scatter plots to compare the intensity distributions of all samples and to assess the gene expression variation between the replicates, respectively. Genes with significant probe sets (FDR<0.1) with ≥2.0-fold changes compared to the corresponding wild-type controls were considered differentially expressed.

Identification and functional annotations of differentially expressed genes regulated by PvSTR1, PvSTIF1 and PvBMY1: Since the genome sequence of switchgrass is not well annotated, a reciprocal BLAST analysis (a common computational method for predicting putative orthologs consisting of two subsequent sets of BLAST analysis) was performed for functional annotation of the differentially expressed genes and their corresponding orthologs. The first BLAST was conducted using the well annotated whole genome sequences of maize, sorghum, rice and Arabidopsis. BLASTN or TBLASTX are generally used for analyses of a polynucleotide sequence, while BLASTP or TBLASTN—for a polypeptide sequence. The first set of BLAST results may optionally be filtered. The full-length sequences of either the filtered results or non-filtered results are then BLASTed back (second BLAST) against sequences from the organism from which the query sequence is derived. The results of the first and second BLASTs are then compared. If this returns the switchgrass gene originally used as the highest scorer, then the two genes are considered putative orthologs.

The numbers of the annotated genes up- or down-regulated by PvSTR1, PvSTIF1 and PvBMY1 in transgenic switchgrass plants are shown in FIG. 11A. A further analysis of the gene expression data revealed that 450, 135, and 619 genes were up-regulated (FIG. 11B) and 165, 164, and 231 genes were down-regulated (FIG. 11C) by PvSTR1, PvSTIF1 and PvBMY1, respectively. Only 1-2 genes were commonly regulated by all three TFs. A relatively small portion of the differentially expressed genes regulated by PvSTIF1 was also regulated by the other two TFs, while more than 280 genes were regulated by both PvSTR1 and PvBMY1 (FIG. 11B-C).

These findings indicate that the transcription factors of the invention regulate the expression of genes involved in key processes and pathways by different mechanisms.

Downstream transcription factors regulated by PvSTR1, PvSTIF1 and PvBMY1: Among the up-regulated genes identified by microarray analysis of transgenic switchgrass lines, 80 were predicted to be transcription factors based on the presence of a DNA-binding domain (Plants TF database v. 3.0). Several of these homologous TF genes have functionally been validated in model and crop plants as regulators of genes involved in economically important agronomic traits, such as biomass production, grain yield and abiotic stress tolerance.

These results confirm that the transcription factors of the current invention appear to function as global transcriptional regulators. The number and variety of the transcription factor genes identified by the microarray analysis indicate that PvSTR1, PvSTIF1 and PvBMY1 regulate key genes in several major pathways and their branches either directly or through downstream transcription factors.

Pathway analysis of differentially expressed genes: For more detailed analysis of the regulatory pattern of the transcription factors of the invention, the differential expression data was used for identification of metabolic and/or signaling pathways or portions of a pathway up-regulated in transgenic switchgrass plants. To investigate the biological functions of differentially expressed genes, gene ontology (GO) analysis was performed to identify the “biological processes category” using a publicly available database (http://bioinfo.cau.edu.cn/agriGO/index.php). The results revealed that PvSTR1 and BMY1 significantly increased the expression of several genes involved in primary metabolic processes, such as photosynthesis and carbohydrate metabolism, and in amino acid and cell wall biosynthesis related pathways, while most of the genes up-regulated by PvSTIF1 were categorized as transcription factors (FIG. 12).

Taken together, the results presented here and in Example 5 indicate that central carbon metabolism in the transgenic plants in which the transcription factors have been over expressed results in major global impact on central carbon metabolism.

Transcriptional regulatory network of the central carbon metabolism in switchgrass: Central carbon metabolism (CCM) is crucial for plant growth and development because of its key role in the generation of accessible energy and primary building blocks for other metabolic pathways. The gene expression analysis of switchgrass lines overexpressing PvSTR1, PvSTIF1 and PvBMY1 revealed a distinctive up-regulation of several genes involved in photosynthesis and carbohydrate metabolism as well as in the primary metabolic processes, which are not only necessary for plant growth and development but often confer highly desirable traits.

Example 8 Transcription Factor-Mediated Modifications of Economically Valuable Traits

The switchgrass transcription factors characterized in this invention (SEQ ID NOs: 1-6) and their homologs (SEQ ID NOs: 7-18) can be introduced into the genome of other plants, including but not limited to the varieties of grain and forage cereals and grasses, oilseeds, biomass crops, legumes, trees, and vegetables. The orthologous genes identified in this invention (see Example 1) can also be used for genetic engineering of economically important crops and model plant systems. It is well known, that transcription factor gene sequences are conserved across different species lines, including plants (Goodrich et al., 1993, Cell 75:519-530; Lin et al., 1991, Nature 353: 569-571). Since the sequences of the switchgrass TFs STR1, STIF1, and BMY1 are related to sequences in other plant species, one skilled in the art can expect that, when expressed in other plants, the switchgrass TF genes and/or their orthologs can have similar effects on plant metabolism and phenotype to those demonstrated herein. For optimal results, both sequential and phylogenetical analyses of the TF genes need to be performed. Since sorghum (Sorghum bicolor L.) and maize (Zea mays L.) are closely related to switchgrass (FIG. 5), both the switchgrass genes and their corresponding orthologs (FIG. 4) can be expressed to increase the photosynthetic activity, to up-regulate the carbon and nitrogen metabolism as well as to improve the stress tolerance of these crops resulting in higher biomass and/or grain production. In sorghum, for example, PvSTR1, PvSTIF1 and PvBMY1 and their respective orthologs with accession numbers XP002463183, XP002452171 and XP002463163 (identified using the methods described in Example 1) would be expected to have similar effects, while in soybean (Glycine max L.), the orthologous genes (accession numbers NP001238200, XP003522453 and XP003546199) would be preferred due to the distant phylogenetic relation between this crop and switchgrass (FIG. 5). In crops with unknown whole genome sequence, orthologous genes from phylogenetically close species can be used. For example, Arabidopsis orthologs of the transcription factors of the invention can be expressed in camelina to achieve the desired trait modification.

The coding sequences can be cloned in expression cassettes and assembled in single- or multi-gene vectors using the methods provided in the invention. Any of the methods for plant transformation described herein can be used to introduce the TF genes into the target plant. For example, particle bombardment with whole plasmids or minimum cassettes can be used for gene delivery to callus cultures initiated from immature zygotic embryos in wheat (Okubara et al., 2002, Theor. Appl. Genet. 106: 74-83) and barley (Wan & Lemaux, 1994, Plant Physiol. 104: 37-48) and to callus induced from immature leaf rolls from sugarcane (Snyman et al., 2006, Plant Cell Rep. 25: 1016-1023) and energy cane (Fouad et al., 2009, In Vitro Cell. Dev. Biol. 45: S74). The expression of switchgrass transcription factors and their orthologs can be engineered by Agrobacterium-mediated transformation in different crops, such as rice (Sahoo et al., 2011, Plant Methods 7:49-60), other small grain crops (reviewed in Shrawat and Lörz, 2006, Plant Biotech. J. 4: 575-603), industrial crops (cotton, Leelavathi et al., 2004, Plant Cell Rep. 22: 465-470; tobacco, Horsch et al., 1985, Science 227: 1229-1231) as well as crops with C₄ photosynthesis, such as maize, sugarcane, sorghum, sweet sorghum, and pearl millet (reviewed in Somleva et al., 2013, Plant Biotech. J. 11: 233-252). The floral dip method can be used for transformation of oilseed crops, such as canola (Li et al., 2010, Int. J. Biol. 2: 127-131) and camelina (Liu et al., 2012, In Vitro Cell. Dev. Biol. 48: 462-468). Both physical and biological transformation methods have been developed for some crops (e.g., soybean, reviewed in Yamada et al., 2012, Breed. Sci. 61: 480-494) and the more efficient method can be used for the purposes of this invention.

Different promoters can be useful for controlling the expression of the TFs of the invention depending on the crop and phenotype of interest. Both constitutive and inducible promoters (responding to environmental, chemical and hormonal signals) can be used. For example, the maize light-inducible cab-m5 promoter is suitable for engineering bioenergy crops, such as switchgrass (Somleva et al., 2008, Plant Biotech. J. 6: 663-678) and sugarcane (Petrasovitch et al., 2012, Plant Biotech J. 10: 569-578) because of its high activity in leaf tissue.

Promoters capable of driving the expression of a TF gene in an organ-specific and developmentally-regulated manner are of a particular interest for modifications of economically valuable traits. The engineered spatiotemporal activity of the transcription factors of the invention can be useful, for example, for increased grain yield in maize, rice, wheat, barley and grain varieties of sorghum, for increased oil content in canola and camelina, and for modifications of the biomass composition in bioenergy crops, such as switchgrass, sugarcane, Miscanthus, sweet sorghum and energy cane. The transcription factor genes of the invention, their homologs and orthologs can be overexpressed in photosynthetic tissues during different stages of embryo and seed development for improvement of grain yield without increasing the production of vegetative biomass. This approach requires the use of promoters with high activity and tightly controlled specificity. Promising candidates are the promoters of the maize genes cyclin delta 2 (Locus #GRMZM2G476685; SEQ ID NO: 22), phospholipase 2A (Locus #GRMZM2G154523; SEQ ID NO: 23), sucrose transporter (Locus #GRMZM2G081589; SEQ ID NO: 24), and cell wall invertase (Locus #GRMZM2G139300; SEQ ID NO: 25) which have been shown to be expressed in leaves but not in the fertilized ovaries at the onset of seed development (Kakumanu et al., 2012, Plant Physiol. 160: 846-847).

Since the genes characterized in the presented invention are global transcriptional regulators, trait modifications can also be achieved through modulating the expression of downstream transcription factors. For example, 10 bZIP transcription factors regulated by the TFs of the invention were identified in transgenic switchgrass by gene expression microarray analysis (see Example 7). Members of the bZIP TF family have been characterized in different plant species and linked to various developmental and physiological processes, such as panicle and seed development, endosperm-specific expression of storage protein genes, vegetative growth and abiotic stress tolerance (reviewed in Nijhawan et al., 2008, Plant Physiol. 146: 333-350). In total, 18 MYB transcription factors regulated by PvSTR1, PvSTIF1 and PvBMY1 were also identified in this study (TABLE 8). Some of these genes are well known for their role in major biological processes—development and cell differentiation, photosynthesis and secondary metabolism, stress tolerance and defense response (reviewed in Ambawat et al., 2013, Physiol. Mol. Biol. Plants 19: 307-321) and can be useful in different approaches to crop improvement.

Example 9 Transformation of Other Crop Species

Agrobacterium-Mediated Transformation of Miscanthus species

Miscanthus has been extensively evaluated as a bioenergy crop in Europe since the early 1980s (Lewandowski et al., 2003, Biomass and Bioenergy, 25: 335-361) and, more recently, in North America (Heaton et al., 2008, Global Change Biology, 14: 2000-2014). The research on biomass productivity and environmental impact has mainly been focused on M. sacchariflorus and Miscanthus x giganteus, a pollen sterile hybrid between M. sacchariflorus and M. sinensis (Jorgensen & Muhs, 2001, In M. B. Jones and M. Walsh (eds.), Miscanthus for energy and fibre. James & James (Science Publishers) Ltd., London, pp. 68-852).

For the development of tissue culture and transformation systems, Miscanthus x giganteus plants established in soil from rhizomes and grown under greenhouse conditions at 27° C. with a 16-hour photoperiod using supplemental sodium halide lamps (200 mol/m²/s) were used as an explant source. Immature inflorescences, axillary meristems, and basal portions of leaves were harvested and used for culture initiation after surface sterilization. The initial explants and resultant cultures were incubated at 27° C., in the dark. Their response to various concentrations and combinations of plant growth regulators and different nitrate-to-ammonium ratios in the tissue culture medium was tested. After 3-4 weeks of culture, the number of explants forming callus was scored and the callus type was determined according to visual appearance and morphogenetic ability. Callus formation was observed from all types of explants with significant differences in the callus induction frequency and the ratio of the callus types formed. The results revealed that immature inflorescences were the best explants for callus initiation and that MS basal medium supplemented with the synthetic auxin 2,4-D as a sole plant growth regulator was optimal for callus initiation, induction of somatic embryo formation and suppression of precocious plant regeneration in these cultures.

Two approaches to improving the medium for callus initiation and growth were used. The experiments were performed with callus cultures propagated by monthly transfers on to MS medium containing 5 mg/L of 2,4-D and 30 g/L sucrose for 6-9 months. To determine the optimal auxin concentration for callus growth, pre-weighed pieces of embryogenic callus (30 pieces per replication, 2 replications per variant) were plated on MS medium supplemented with 1, 2, 3, 4, and 5 mg/L of 2,4-D. Cultures grown on MS medium without any plant growth regulators served as a control. After 4 weeks, all calluses were weighed and their growth rate was calculated as %=[(callus final fresh weight−callus initial fresh weight)/callus initial fresh weight]×100. Since the highest growth rate was detected in the presence of 2 mg/L of 2,4-D, this concentration was used for callus initiation, propagation and selection in the transformation experiments.

For further optimization of the tissue culture procedure, the effects of several anti-necrotic compounds on callus growth and embryogenic response were evaluated. Briefly, pre-weighed embryogenic callus (27-77 mg fresh weight per replication, 2 replications per variant) was plated on MS medium containing 2 mg/L 2,4-D and supplemented with ascorbic acid (15 mg/L), cysteine (40 mg/L), and silver nitrate (5 mg/L) alone or in different combinations. Culture growth and development were monitored on a weekly basis and callus growth rate was calculated as described above after 4 weeks. The results showed that callus growth was promoted by ascorbic acid and cysteine and not affected by silver nitrate. Although the highest growth rate was detected in calluses grown in the presence of all three anti-necrotic compounds, some undesired changes in the development of these cultures were also observed. Taken together, the results demonstrated that MS medium supplemented with 2 mg/L of 2,4-D, 15 mg/L of ascorbic acid and 40 mg/L of cysteine was optimal for the growth and development of embryogenic callus cultures.

Since young, developing panicles proved to be an excellent source of explants for callus initiation in Miscanthus x giganteus, these studies were further extended in order to develop a novel protocol for in vitro production of immature inflorescences and callus initiation from them. The possibility for vegetative propagation by node cultures was also explored. The top culm node and the nodes below the top one of tillers prior to flowering from plants grown under greenhouse conditions were used as explant sources. After surface sterilization, the nodal segments were incubated in a 10% aqueous solution of polyvinylpyrrolidone (PVP40, Sigma), split longitudinally and plated on to MS medium containing 10 mg/L BAP and 30 g/L sucrose. Individual spikelets from panicles formed from the top node were plated on the optimized medium for callus initiation described above. Resultant calluses were propagated by transfers every 3-4 weeks on to a fresh medium and used in transformation experiments. For plant regeneration, calluses initiated from in vitro developed panicles were plated on hormone-free MS medium and incubated at 27° C. with a 16 h photoperiod (cool white fluorescent bulbs, 80 μmol/m²/s) and subcultured every 3-4 weeks. Plantlets with 3-4 leaves were transferred to larger tissue culture containers with the same medium and grown for another 2-3 weeks prior to transfer to soil.

Shoots produced from nodal segments below the top node were also cultured on hormone-free MS medium for 3-4 weeks prior to transfer to soil.

Agrobacterium-mediated transformation of established embryogenic callus cultures initiated from in vitro developed panicles was performed following the previously described procedure for switchgrass transformation (Somleva, 2006, Agrobacterium Protocols Wang K., ed., pp 65-74: Humana Press; Somleva et al., 2002, Crop Sci. 42: 2080-2087) with the following modifications: infected cultures were co-cultivated with Agrobacterium tumefaciens for 5-10 days prior to transfer to a medium supplemented with 3 mg/L bialaphos for callus selection. Using the developed methods, Miscanthus species can be engineered with the transcription factor genes of the invention for increased production of biomass and/or modifications of its composition for bioenergy applications.

Miscanthus sinensis callus cultures were initiated from mature caryopses and their embryogenic potential was evaluated as described previously for switchgrass (U.S. Pat. No. 8,487,159 to Somleva et al.). They were transformed following the procedure for Agrobacterium-mediated transformation of switchgrass (Somleva, 2006, Agrobacterium Protocols Wang K., ed., pp 65-74: Humana Press; Somleva et al., 2002, Crop Sci. 42: 2080-2087).

Agrobacterium-Mediated Transformation of Maize

The binary vectors provided in the invention can be used for Agrobacterium-mediated transformation of maize following a previously described procedure (Frame et al., 2006, Agrobacterium Protocols Wang K., ed., Vol. 1, pp 185-199, Humana Press).

Plant material: Plants grown in a greenhouse are used as an explant source. Ears are harvested 9-13 d after pollination and surface sterilized with 80% ethanol.

Explant isolation, infection and co-cultivation: Immature zygotic embryos (1.2-2.0 mm) are aseptically dissected from individual kernels and incubated in A. tumefaciens strain EHA101 culture (grown in 5 ml N6 medium supplemented with 100 μM acetosyringone for stimulation of the bacterial vir genes for 2-5 h prior to transformation) at room temperature for 5 min. The infected embryos are transferred scutellum side up on to a co-cultivation medium (N6 agar-solidified medium containing 300 mg/l cysteine, 5 μM silver nitrate and 100 μM acetosyringone) and incubated at 20° C., in the dark for 3 d. Embryos are transferred to N6 resting medium containing 100 mg/l cefotaxime, 100 mg/l vancomycin and 5 μM silver nitrate and incubated at 28° C., in the dark for 7 d.

Callus selection: All embryos are transferred on to the first selection medium (the resting medium described above supplemented with 1.5 mg/l bialaphos) and incubated at 28° C., in the dark for 2 weeks followed by subculture on a selection medium containing 3 mg/l bialaphos. Proliferating pieces of callus are propagated and maintained by subculture on the same medium every 2 weeks.

Plant regeneration and selection: Bialaphos-resistant embryogenic callus lines are transferred on to regeneration medium I (MS basal medium supplemented with 60 g/l sucrose, 1.5 mg/l bialaphos and 100 mg/l cefotaxime and solidified with 3 g/l Gelrite) and incubated at 25° C., in the dark for 2 to 3 weeks. Mature embryos formed during this period are transferred on to regeneration medium II (the same as regeneration medium I with 3 mg/l bialaphos) for germination in the light (25° C., 80-100 μE/m²/s light intensity, 16/8-h photoperiod). Regenerated plants are ready for transfer to soil within 10-14 days.

Agrobacterium-Mediated Transformation of Sorghum

The vectors provided in the invention can be used for sorghum transformation following a previously described procedure (Zhao, 2006, Agrobacterium Protocols Wang K., ed., Vol. 1, pp 233-244, Humana Press).

Plant material: Plants grown under greenhouse, growth chamber or field conditions are used as an explant source. Immature panicles are harvested 9-12 d post pollination and individual kernels are surface sterilized with 50% bleach for 30 min followed by three washes with sterile distilled water.

Explant isolation, infection and co-cultivation: Immature zygotic embryos (1-1.5 mm) are aseptically dissected from individual kernels and incubated in A. tumefaciens strain LBA4404 suspension in PHI-I liquid medium (MS basal medium supplemented with 1 g/l casamino acids, 1.5 mg/l 2,4-D, 68.5 g/l sucrose, 36 g/l glucose and 100 μM acetosyringone) at room temperature for 5 min. The infected embryos are transferred with embryonic axis down on to a co-cultivation PHI-T medium (agar-solidified modified PHI-I medium containing 2.0 mg/l 2,4-D, 20 g/l sucrose, 10 g/l glucose, 0.5 g/l MES, 0.7 g/l proline, 10 mg/l ascorbic acid and 100 μM acetosyringone) and incubated at 25° C., in the dark for 3 d. For resting, embryos are transferred to the same medium (without acetosyringone) supplemented with 100 mg/l carbenicillin and incubated at 28° C., in the dark for 4 d.

Callus selection: Embryos are transferred on to the first selection medium PHI-U (PHI-T medium described above supplemented with 1.5 mg/l 2,4-D, 100 mg/l carbenicillin and 5 mg/l PPT without glucose and acetosyringone) and incubated at 28° C., in the dark for 2 weeks followed by subculture on a selection medium containing 10 mg/l PPT. Proliferating pieces of callus are propagated and maintained by subculture on the same medium every 2 weeks for the remainder of the callus selection process of 10 weeks.

Plant regeneration and selection: Herbicide-resistant callus is transferred on to regeneration medium I (PHI-U medium supplemented with 0.5 mg/l kinetin) and incubated at 28° C., in the dark for 2 to 3 weeks for callus growth and embryo development. Cultures are transferred on to regeneration medium II (MS basal medium with 0.5 mg/l zeatin, 700 mg/l proline, 60 g/l sucrose and 100 mg/l carbenicillin) for shoot formation (28° C., in the dark). After 2-3 weeks, shoots are transferred on to a rooting medium (regeneration II medium supplemented with 20 g/l sucrose, 0.5 mg/l NAA and 0.5 mg/l IBA) and grown at 25° C., 270 μE/m²/s light intensity with a 16/8-h photoperiod. When the regenerated plants are 8-10 cm tall, they can be transferred to soil and grown under greenhouse conditions.

Agrobacterium-Mediated Transformation of Barley

The vectors provided in the invention can be used for transformation of barley as described by Tingay et al., 1997, Plant J. 11: 1369-1376.

Plant material: Plants of the spring cultivar Golden Promise are grown under greenhouse or growth chamber conditions at 18° C. with a 16/8 hours photoperiod. Spikes are harvested when the zygotic embryos are 1.5-2.5 mm in length. Developing caryopses are sterilized with sodium hypochlorite (15 w/v chlorine) for 10 min and rinsed four times with sterile water.

Explant Isolation, Infection and Co-Cultivation:

Immature zygotic embryos are aseptically dissected from individual kernels and after removal of the embryonic axes are placed scutellum side up on a callus induction medium (Gelrite-solidified MS basal medium containing 30 g/l maltose, 1.0 g/l casein hydrolysate, 0.69 g/l proline and 2.5 mg/L dicamba. Embryos are incubated at 24° C. in the dark during subsequent culture. One day after isolation, the embryos are incubated in A. tumefaciens strain AGL1 culture (grown from a single colony in MG/L medium) followed by a transfer on to the medium described above.

Callus Selection:

After co-cultivation for 2-3 d, embryos are transferred on to the callus induction medium supplemented with 3 mg/l bialaphos and 150 mg/l Timentin. Cultures are selected for about 2 months with transfers to a fresh selection medium every 2 weeks.

Plant Regeneration and Selection:

Bialaphos-resistant embryogenic callus lines are transferred to a Phytagel-solidified regeneration medium containing 1 mg/l BA and 3 mg/l bialaphos for selection of transgenic plants and grown at 24° C. under fluorescent lights with a 16/8 h photoperiod. For root development, regenerated plants are transferred to a hormone-free callus induction medium supplemented with 1 mg/l bialaphos. After development of a root system, plants are transferred to soil and grown in a greenhouse or a growth chamber under the conditions described above.

Agrobacterium-Mediated Transformation of Rice

The binary vectors provided in the invention can be used for Agrobacterium-mediated transformation of rice following a previously described procedure (Herve and Kayano, 2006, Agrobacterium Protocols Wang K., ed., Vol. 1, pp 213-222, Humana Press).

Plant material: Mature seeds from japonica rice varieties grown in a greenhouse are used as an explant source.

Culture transformation and selection: Dehusked seeds are surface sterilized with 70% ethanol for 1 min and 3% sodium hypochlorite for 30 min followed by six washes with sterile distilled water. Seeds are plated embryo side up on an induction medium (Gelrite-solidified N6 basal medium supplemented with 300 mg/l casamino acids, 2.88 g/l proline, 30 g/l sucrose and 2 mg/l 2,4-D) and incubated at 32° C., under continuous light for 5 d. Germinated seeds with swelling of the scutellum are infected with A. tumefaciens strain LBA4404 (culture from 3-day-old plates resuspended in N6 medium supplemented with 100 μM acetosyringone, 68.5 g/l sucrose and 36 g/l glucose) at room temperature for 2 min followed by transfer on to a co-cultivation medium (N6 Gelrite-solidified medium containing 300 mg/l casamino acids, 30 g/l sucrose, 10 g/l glucose, 2 mg/l 2,4-D and 100 μM acetosyringone) and incubation at 25° C., in the dark for 3 d.

For selection of transformed embryogenic tissues, whole seedlings washed with 250 mg/l cephotaxine are transferred on to N6 agar-solidified medium containing 300 mg/l casamino acids, 2.88 g/l proline, 30 g/l sucrose, 2 mg/l 2,4-D, 100 mg/l cefotaxime, 100 mg/l vancomycin and 35 mg/l G418 disulfate). Cultures are incubated at 32° C., under continuous light for 2-3 weeks.

Plant regeneration and selection: Resistant proliferating calluses are transferred on to agar-solidified N6 medium containing 300 mg/l casamino acids, 500 mg/l proline, 30 g/l sucrose, 1 mg/l NAA, 5 mg/l ABA, 2 mg/l kinetin, 100 mg/l cefotaxime, 100 mg/l vancomycin and 20 mg/l G418 disulfate. After one week of growth at 32° C., under continuous light, the surviving calluses are transferred on to MS medium (solidified with 10 g/l agarose) supplemented with 2 g/l casamino acids, 30 g/l sucrose, 30 g/l sorbitol, 0.02 mg/l NAA, 2 mg/l kinetin, 100 mg/l cefotaxime, 100 mg/l vancomycin and 20 mg/l G418 disulfate and incubated under the same conditions for another week followed by a transfer on to the same medium with 7 g/l agarose. After 2 weeks, the emerging shoots are transferred on to Gelrite-solidified MS hormone-free medium containing 30 g/l sucrose and grown under continuous light for 1-2 weeks to promote shoot and root development. When the regenerated plants are 8-10 cm tall, they can be transferred to soil and grown under greenhouse conditions. After about 10-16 weeks, transgenic seeds are harvested.

Indica rice varieties are transformed with Agrobacterium following a similar procedure (Datta and Datta, 2006, Agrobacterium Protocols Wang K., ed., Vol. 1, pp 201-212, Humana Press).

Microprojectile Bombardment-Mediated Transformation of Sugarcane

An expression cassette containing a transcription factor gene can be co-introduced with a cassette of a marker gene (e.g., npt) into sugarcane via biolistics following a previously described protocol (Taparia et al., 2012, In Vitro Cell. Dev. Biol. 48: 15-22))

Plant material: Greenhouse-grown plants with 6-8 visible nodes are used as an explant source. Tops are collected and surface sterilized with 70% ethanol. The outermost leaves are removed under aseptic conditions and immature leaf whorl cross sections (about 2 mm) are cut from the region 1-10 cm above the apical node.

Culture initiation, transformation and selection: The isolated leaf sections are cultured on MS basal media supplemented with 20 g/l sucrose, 1.86 mg/l p-chlorophenoxyacetic acid (CPA), 1.86 mg/l NAA and 0.09 mg/l BA at 28° C., under 30 μmol/m²/s light intensity and a 16/8-h photoperiod for 7 d. Embryogenic cultures are subcultured to fresh medium and used for transformation.

For microprojectile bombardment, leaf disks are plated on the culture initiation medium supplemented with 0.4 M sorbitol 4 hours before gene transfer. Plasmid DNA (200 ng) containing the expression cassettes of a TF and a marker gene is precipitated onto 1.8 mg gold particles (0.6 μm) following a previously described procedure (Altpeter and Sandhu, 2010, Genetic transformation—biolistics, Davey & Anthony eds., pp 217-237, Wiley, Hoboken). The DNA (10 ng per shot) is delivered to the explants by a PDS-1000 Biolistc particle delivery system (Biorad) using 1100-psi rupture disk, 26.5 mmHg chamber vacuum and a shelf distance of 6 cm. pressure). The bombarded explants are transferred to the culture initiation medium described above and incubated for 4 days.

For selection, cultures are transferred on to the initiation medium supplemented with 30 mg/l geneticin and incubated for 10 d followed by another selection cycle under the same conditions.

Plant regeneration and selection: Cultures are transferred on to the selection medium described above without CPA and grown at 28° C., under 100 μmol/m²/s light intensity with a 16/8-h photoperiod. Leaf disks with small shoots (about 0.5 cm) are plated on a hormone-free medium with 30 mg/l geneticin for shoot growth and root development. Prior to transfer to soil, roots of regenerated plants can be dipped into a commercially available root promoting powder.

Transformation of Wheat by Microprojectile Bombardment

The gene constructs provided in the invention can be used for wheat transformation by microprojectile bombardment following a previously described protocol (Weeks et al., 1993, Plant Physiol. 102: 1077-1084).

Plant material: Plants from the spring wheat cultivar Bobwhite are grown at 18-20° C. day and 14-16° C. night temperatures under a 16 h photoperiod. Spikes are collected 10-12 weeks after sowing (12-16 days post anthesis). Individual caryopses at the early-medium milk stage are sterilized with 70% ethanol for 5 min and 20% sodium hypochlorite for 15 min followed by three washes with sterile water.

Culture initiation, transformation and selection: Immature zygotic embryos (0.5-1.5 mm) are dissected under aseptic conditions, placed scutellum side up on a culture induction medium (Phytagel-solidified MS medium containing 20 g/l sucrose and 1.5 mg/l 2,4-D) and incubated at 27° C., in the light (43 μmol/m²/s) for 3-5 d.

For microprojectile bombardment, embryo-derived calluses are plated on the culture initiation medium supplemented with 0.4 M sorbitol 4 hours before gene transfer. Plasmid DNA containing the expression cassettes of a TF and the marker gene bar is precipitated onto 0.6-μm gold particles and delivered to the explants as described for sugarcane.

The bombarded explants are transferred to callus selection medium (the culture initiation medium described above containing 1-2 mg/l bialaphos) and subcultured every 2 weeks.

Plant regeneration and selection: After one-two selection cycles, cultures are transferred on to MS regeneration medium supplemented with 0.5 mg/l dicamba and 2 mg/l bialaphos. For root formation, the resulting bialaphos-resistant shoots are transferred to hormone-free half-strength MS medium. Plants with well-developed roots are transferred to soil and acclimated to lower humidity at 21° C. with a 16-h photoperiod (300 μmol/m²/s) for about 2 weeks prior to transfer to a greenhouse.

Agrobacterium-Mediated Transformation of Camelina

The gene constructs provided in the invention can be used for camelina transformation by floral dip following a previously described protocol (International Patent Application WO 2011034946).

Plant material: Plants grown from seeds under greenhouse conditions (24° C./18° C. day/night temperatures) with unopened flower buds are used for floral dip transformation.

Agrobacterium culture preparation and plant inoculation: The constructs of interest are introduced into Agrobacterium strain GV3101 by electroporation. A single colony of GV3101 is obtained from a freshly streaked plate and is inoculated into 5 mL LB medium. After overnight growth at 28° C., 2 ml of culture is transferred to a 500-mL flask containing 300 ml of LB and incubated overnight at 28° C. Cells are pelleted by centrifugation (6000 rpm, 20 min) and diluted to an OD₆₀₀ 0.8 with the infiltration medium containing 5% sucrose and 0.05% (v/v) Silwet-L77 (Lehle Seeds, Round Rock, Tex., USA). Camelina plants are transformed as follows. Pots containing plants at the flowering stage are placed in a vacuum desiccator (Bel-Art, Pequannock, N.J., USA) and their inflorescences are immersed into the Agrobacterium culture. A vacuum (85 kPa) is applied for 5 min. Plants are removed from the desiccators, covered with plastic bags and kept at room temperature, in the dark for 24 h. Plants are grown in a greenhouse for seed formation.

Identification of transgenic seeds: To identify bialaphos-resistant seeds, seeds from inoculated plants are harvested, sterilized with 70% ethanol and 10% bleach followed by washes with sterile water. Sterilized seeds are placed on germination and selection medium (half-strength MS basal medium) containing 10 mg/L bialaphos and incubated in a growth chamber at 23/20° C. (day/night) with a 16-h photoperiod (3000 lux). Seedlings with green cotyledons are transferred to soil about six days after initiation of germination.

Agrobacterium-Mediated Transformation of Brassica Napus

Plant material: Mature seeds are surface sterilized in 10% commercial bleach for 30 min with gentle shaking and washed three times with sterile distilled water.

Culture initiation and transformation: Seeds are plated on germination medium (MS basal medium supplemented with 30 g/l sucrose) and incubated at 24° C. with a 16-h photoperiod at a light intensity of 60-80 μE/m²/s for 4-5 d. For transformation, cotyledons with ˜2 mm of the petiole at the base are excised from the resulting seedlings, immersed in Agrobacterium tumefaciens strain EHA101 suspension (grown from a single colony in 5 ml of minimal medium supplemented with appropriate antibiotics at 28° C. for 48 h) for 1 s and immediately embedded to a depth of ˜2 mm in a co-cultivation medium (MS basal medium with 30 g/l sucrose and 20 μM benzyladenine). The inoculated cotyledons are incubated under the same growth conditions for 48 h.

Plant regeneration and selection: After co-cultivation, cotyledons are transferred on to a regeneration medium comprising MS medium supplemented with 30 g/l sucrose and 20 μM benzyladenine, 300 mg/l timentin and 20 mg/l kanamycin sulfate. After 2-3 weeks, regenerated shoots are cut and maintained on MS medium for shoot elongation containing 30 g/l sucrose, 300 mg/l timentin, and 20 mg/l kanamycin sulfate. The elongated shoots are transferred to a rooting medium comprising MS basal medium supplemented with 30 g/l sucrose, 2 mg/l indole butyric acid (IBA) and 500 mg/L carbenicillin. After root formation, plants are transferred to soil and grown to seed maturity under growth chamber or greenhouse conditions.

Agrobacterium-Mediated Transformation of Soybean

The soybean orthologs of the switchgrass transcription factor genes identified in the invention (FIG. 4) are assembled in binary vectors (TABLE 9) and used for Agrobacterium-mediated transformation of soybean following a previously described procedure (Ko et al., 2006, Agrobacterium Protocols Wang K., ed., Vol. 1, pp 397-405, Humana Press).

Plant material: Immature seeds from soybean plants grown under greenhouse or field conditions are used as an explant source. Young pods are harvested and surface sterilized with 70% 2-propanol for 30 sec and 25% Clorox for 20 min followed by three washes with sterile distilled water.

Culture transformation and selection: Under aseptic conditions, immature seeds are removed from the pods and the cotyledons are separated from the seed coat followed by incubation in A. tumefaciens culture (grown from a single colony at 28° C., overnight) in co-cultivation medium (MS salts and B5 vitamins) supplemented with 30 g/l sucrose, 40 mg/l 2,4-D and 40 mg/l acetosyringone for 60 min. Infected explants are plated abaxial side up on agar-solidified co-cultivation medium and incubated at 25° C., in the dark for 4 d.

For selection of transformed tissues, cotyledons washed with 500 mg/l cephotaxine are placed abaxial side up on a medium for induction of somatic embryo formation (Gelrite-solidified MS medium containing 30 g/l sucrose, 40 mg/l 2,4-D, 500 mg/l cefotaxime, and 10 mg/l hygromycin) and incubated at 25° C., under a 23-h photoperiod (10-20 μE/m²/s) for 2 weeks. After another two weeks of growth under the same conditions in the presence of 25 mg/l hygromycin, the antibiotic-resistant somatic embryos are transferred on MS medium for embryo maturation supplemented with 60 g/l maltose, 500 mg/l cefotaxime, and 10 mg/l hygromycin and grown under the same conditions for 8 weeks with 2-week subculture intervals.

Plant regeneration and selection: The resulting cotyledonary stage embryos are desiccated at 25° C., under a 23-h photoperiod (60-80 μE/m²/s) for 5-7 d followed by culture on MS regeneration medium containing 30 g/l sucrose and 500 mg/l cefotaxime for 4-6 weeks for shoot and root development. When the plants are 5-10 cm tall, they are transferred to soil and grown in a greenhouse after acclimatization for 7 d.

TABLE 9 Plant transformation vectors for overexpression of the orthologous transcription factor genes GmSTR1, GmSTIF1 and GmBMY1 in soybean. Vector ID* TF gene/marker Annotation SEQ ID Coordinates (bp) pMBXS884 GmSTR1/hpt Agrobacterium T-DNA right border 26 12780-12805 CaMV35S promoter to drive GmSTR1gene  9566-11260 GmSTR1coding region 11269-12124 nos terminator 12258-12532 CaMV35S promoter to drive hptII gene 7707-9292 hptII coding region 6456-7692 CaMV35S polyA terminator 6248-6450 Agrobacterium T-DNA left border 6173-6198 pMBXS885 GmSTIF1/hpt Agrobacterium T-DNA right border 27 12384-12409 CaMV35S promoter to drive GmSTIF1gene  9566-11260 GmSTIF1 coding region 11269-12055 nos terminator 11862-12136 CaMV35S promoter to drive hptII gene 7707-9292 hptII coding region 6456-7692 CaMV35S polyA terminator 6248-6450 Agrobacterium T-DNA left border 6173-6198 pMBXS886 GmBMY1/hpt Agrobacterium T-DNA right border 28 12459-12484 CaMV35S promoter to drive GmBMY1gene  9566-11260 GmBMY1coding region 11269-11782 nos terminator 11937-12211 CaMV35S promoter to drive hptII gene 7707-9292 hptII coding region 6456-7692 CaMV35S polyA terminator 6248-6450 Agrobacterium T-DNA left border 6173-6198 *All vectors are based on the transformation vector pCambia3300 found on the world wide web at cambia.org; the hpt gene (conferring resistance to hygromycin) is used as a marker for selection of transformed explants and plants.

The teachings of all patents, published applications and references cited herein are incorporated by reference in their entirety.

While this invention has been particularly shown and described with references to example embodiments thereof, it will be understood by those skilled in the art that various changes in form and details may be made therein without departing from the scope of the invention encompassed by the appended claims. 

What is claimed is:
 1. A method for producing a genetically modified plant or plant cell having an increased carbon flow, the method comprising: a) transforming one or more host plants or plant cells with a vector comprising a nucleic acid encoding a polypeptide having at least 60% identity to SEQ ID NO: 4 operably linked to a promoter; and (b) selecting one or more transformed plants or plant cells for increased carbon flow by selecting for one or more of increased biomass yield, increased starch yield, increased glucose content, or increased sucrose content as compared to a control plant lacking the vector.
 2. The method according to claim 1, the method further comprising collecting seeds comprising the vector from the selected plant.
 3. The method according to claim 1, the method further comprising regenerating a plant from the selected plant cell and collecting seeds comprising the vector from the regenerated plant.
 4. The method of claim 1, wherein the selected plant further exhibits increased tolerance to one or more abiotic stress factors of excess or deficiency of water and/or light, high or low temperature, or high salinity, as compared to a control plant lacking the vector.
 5. The method of claim 1, wherein the promoter is light inducible.
 6. The method of claim 1, wherein the promoter comprises positions 8951 to 10645 of SEQ ID NO:
 21. 7. The method of claim 1, wherein the host plant is a monocotyledonous plant or a dicotyledenous plant.
 8. The method of claim 7, wherein the host plant is switchgrass.
 9. The method of claim 7, wherein the host plant is maize.
 10. The method of claim 7, wherein the host plant is sugar cane.
 11. The method according to claim 1, wherein the host plant is Miscanthus, Medicago, sweet sorghum, grain sorghum, sugar cane, energy cane, elephant grass, maize, wheat, barley, oat, rice, soybean, oil palm, safflower, sesame, flax, cotton, sunflower, Camelina, Brassica napus, Brassica carinata, Brassica juncea, pearl millet, or foxtail millet.
 12. The method of claim 1, wherein the polypeptide has at least 70% sequence identity to SEQ ID NO:
 4. 13. The method of claim 1, wherein the polypeptide has at least 80% sequence identity to SEQ ID NO:
 4. 14. The method of claim 1, wherein the polypeptide has at least 85% sequence identity to SEQ ID NO:
 4. 15. The method of claim 1, wherein the polypeptide has at least 90% sequence identity to SEQ ID NO:
 4. 16. The method of claim 1, wherein the polypeptide has at least 95% sequence identity to SEQ ID NO:
 4. 17. The method of claim 1, wherein the polypeptide has at least 99% sequence identity to SEQ ID NO:
 4. 18. The method of claim 17, wherein the host plant is Miscanthus, Medicago, sweet sorghum, grain sorghum, sugar cane, energy cane, elephant grass, maize, wheat, barley, oat, rice, soybean, oil palm, safflower, sesame, flax, cotton, sunflower, Camelina, Brassica napus, Brassica carinata, Brassica juncea, pearl millet, or foxtail millet.
 19. The method of claim 1, wherein the polypeptide comprises SEQ ID NO:
 4. 20. The method of claim 19, wherein the host plant is Miscanthus, Medicago, sweet sorghum, grain sorghum, sugar cane, energy cane, elephant grass, maize, wheat, barley, oat, rice, soybean, oil palm, safflower, sesame, flax, cotton, sunflower, Camelina, Brassica napus, Brassica carinata, Brassica juncea, pearl millet, or foxtail millet. 